Usage: STAR  [options]... --genomeDir /path/to/genome/index/   --readFilesIn R1.fq R2.fq
Spliced Transcripts Alignment to a Reference (c) Alexander Dobin, 2009-2022

STAR version=2.7.11b
STAR compilation time,server,dir=2024-02-11T19:36:26+00:00 :/tmp/STAR-2.7.11b/source
For more details see:
<https://github.com/alexdobin/STAR>
<https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf>
### versions
versionGenome           2.7.4a
    string: earliest genome index version compatible with this STAR release. Please do not change this value!

### Parameter Files
parametersFiles          -
    string: name of a user-defined parameters file, "-": none. Can only be defined on the command line.

### System
sysShell            -
    string: path to the shell binary, preferably bash, e.g. /bin/bash.
                    - ... the default shell is executed, typically /bin/sh. This was reported to fail on some Ubuntu systems - then you need to specify path to bash.

### Run Parameters
runMode                         alignReads
    string: type of the run.
                                alignReads             ... map reads
                                genomeGenerate         ... generate genome files
                                inputAlignmentsFromBAM ... input alignments from BAM. Presently only works with --outWigType and --bamRemoveDuplicates options.
                                liftOver               ... lift-over of GTF files (--sjdbGTFfile) between genome assemblies using chain file(s) from --genomeChainFiles.
                                soloCellFiltering  </path/to/raw/count/dir/>   </path/to/output/prefix>    ... STARsolo cell filtering ("calling") without remapping, followed by the path to raw count directory and output (filtered) prefix

runThreadN                      1
    int: number of threads to run STAR

runDirPerm                      User_RWX
    string: permissions for the directories created at the run-time.
                                User_RWX ... user-read/write/execute
                                All_RWX  ... all-read/write/execute (same as chmod 777)

runRNGseed                      777
    int: random number generator seed.


### Genome Parameters
genomeDir                   ./GenomeDir/
    string: path to the directory where genome files are stored (for --runMode alignReads) or will be generated (for --runMode generateGenome)

genomeLoad                NoSharedMemory
    string: mode of shared memory usage for the genome files. Only used with --runMode alignReads.
                          LoadAndKeep     ... load genome into shared and keep it in memory after run
                          LoadAndRemove   ... load genome into shared but remove it after run
                          LoadAndExit     ... load genome into shared memory and exit, keeping the genome in memory for future runs
                          Remove          ... do not map anything, just remove loaded genome from memory
                          NoSharedMemory  ... do not use shared memory, each job will have its own private copy of the genome

genomeFastaFiles            -
    string(s): path(s) to the fasta files with the genome sequences, separated by spaces. These files should be plain text FASTA files, they *cannot* be zipped.
                            Required for the genome generation (--runMode genomeGenerate). Can also be used in the mapping (--runMode alignReads) to add extra (new) sequences to the genome (e.g. spike-ins).

genomeChainFiles            -
    string: chain files for genomic liftover. Only used with --runMode liftOver .

genomeFileSizes             0
    uint(s)>0: genome files exact sizes in bytes. Typically, this should not be defined by the user.
    
genomeTransformOutput       None
    string(s):              which output to transform back to original genome
                            SAM     ... SAM/BAM alignments
                            SJ      ... splice junctions (SJ.out.tab)
                            Quant   ... quantifications (from --quantMode option)
                            None    ... no transformation of the output        

genomeChrSetMitochondrial   chrM M MT
    string(s):              names of the mitochondrial chromosomes. Presently only used for STARsolo statistics output/

### Genome Indexing Parameters - only used with --runMode genomeGenerate
genomeChrBinNbits           18
    int: =log2(chrBin), where chrBin is the size of the bins for genome storage: each chromosome will occupy an integer number of bins. For a genome with large number of contigs, it is recommended to scale this parameter as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)]).

genomeSAindexNbases         14
    int: length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1).

genomeSAsparseD             1
    int>0: suffux array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction

genomeSuffixLengthMax       -1
    int: maximum length of the suffixes, has to be longer than read length. -1 = infinite.
    
genomeTransformType         None
    string: type of genome transformation
                            None       ... no transformation
                            Haploid    ... replace reference alleles with alternative alleles from VCF file (e.g. consensus allele)
                            Diploid    ... create two haplotypes for each chromosome listed in VCF file, for genotypes 1|2, assumes perfect phasing (e.g. personal genome)

genomeTransformVCF          -
    string: path to VCF file for genome transformation


    
#####UnderDevelopment_begin : not supported - do not use
genomeType                  Full
    string: type of genome to generate
                            Full                ... full (normal) genome
                            Transcriptome       ... genome consists of transcript sequences
                            SuperTransriptome   ... genome consists of superTranscript sequences
#####UnderDevelopment_end

# DEPRECATED: please use --genomeTransformVCF and --genomeTransformType options instead.
#genomeConsensusFile         -
#    string: VCF file with consensus SNPs (i.e. alternative allele is the major (AF>0.5) allele)
# DEPRECATED 



### Splice Junctions Database
sjdbFileChrStartEnd                     -
    string(s): path to the files with genomic coordinates (chr <tab> start <tab> end <tab> strand) for the splice junction introns. Multiple files can be supplied and will be concatenated.

sjdbGTFfile                             -
    string: path to the GTF file with annotations

sjdbGTFchrPrefix                        -
    string: prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL annotations with UCSC genomes)

sjdbGTFfeatureExon                      exon
    string: feature type in GTF file to be used as exons for building transcripts

sjdbGTFtagExonParentTranscript          transcript_id
    string: GTF attribute name for parent transcript ID (default "transcript_id" works for GTF files)

sjdbGTFtagExonParentGene                gene_id
    string: GTF attribute name for parent gene ID (default "gene_id" works for GTF files)

sjdbGTFtagExonParentGeneName            gene_name
    string(s): GTF attribute name for parent gene name

sjdbGTFtagExonParentGeneType            gene_type gene_biotype
    string(s): GTF attribute name for parent gene type

sjdbOverhang                            100
    int>0: length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)

sjdbScore                               2
    int: extra alignment score for alignments that cross database junctions

sjdbInsertSave                          Basic
    string: which files to save when sjdb junctions are inserted on the fly at the mapping step
                    Basic ... only small junction / transcript files
                    All   ... all files including big Genome, SA and SAindex - this will create a complete genome directory

### Variation parameters
varVCFfile                              -
    string: path to the VCF file that contains variation data. The 10th column should contain the genotype information, e.g. 0/1

### Input Files
inputBAMfile                -
    string: path to BAM input file, to be used with --runMode inputAlignmentsFromBAM

### Read Parameters
readFilesType               Fastx
    string: format of input read files
                            Fastx       ... FASTA or FASTQ
                            SAM SE      ... SAM or BAM single-end reads; for BAM use --readFilesCommand samtools view
                            SAM PE      ... SAM or BAM paired-end reads; for BAM use --readFilesCommand samtools view
                            
readFilesSAMattrKeep        All
    string(s): for --readFilesType SAM SE/PE, which SAM tags to keep in the output BAM, e.g.: --readFilesSAMtagsKeep RG PL
                            All     ... keep all tags
                            None    ... do not keep any tags

readFilesIn                 Read1 Read2
    string(s): paths to files that contain input read1 (and, if needed,  read2)

readFilesManifest           -
    string: path to the "manifest" file with the names of read files. The manifest file should contain 3 tab-separated columns:
            paired-end reads: read1_file_name $tab$ read2_file_name $tab$ read_group_line.
            single-end reads: read1_file_name $tab$ -               $tab$ read_group_line.
            Spaces, but not tabs are allowed in file names.
            If read_group_line does not start with ID:, it can only contain one ID field, and ID: will be added to it.
            If read_group_line starts with ID:, it can contain several fields separated by $tab$, and all fields will be be copied verbatim into SAM @RG header line.

readFilesPrefix             -
    string: prefix for the read files names, i.e. it will be added in front of the strings in --readFilesIn

readFilesCommand             -
    string(s): command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout
               For example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc.

readMapNumber               -1
    int: number of reads to map from the beginning of the file
                            -1: map all reads

readMatesLengthsIn          NotEqual
    string: Equal/NotEqual - lengths of names,sequences,qualities for both mates are the same  / not the same. NotEqual is safe in all situations.

readNameSeparator           /
    string(s): character(s) separating the part of the read names that will be trimmed in output (read name after space is always trimmed)

readQualityScoreBase        33
    int>=0: number to be subtracted from the ASCII code to get Phred quality score

### Read Clipping

clipAdapterType             Hamming
    string:                 adapter clipping type
                            Hamming ... adapter clipping based on Hamming distance, with the number of mismatches controlled by --clip5pAdapterMMp
                            CellRanger4 ... 5p and 3p adapter clipping similar to CellRanger4. Utilizes Opal package by Martin Šošić: https://github.com/Martinsos/opal
                            None ... no adapter clipping, all other clip* parameters are disregarded
                            
clip3pNbases                 0
    int(s): number(s) of bases to clip from 3p of each mate. If one value is given, it will be assumed the same for both mates.

clip3pAdapterSeq            -
    string(s): adapter sequences to clip from 3p of each mate.  If one value is given, it will be assumed the same for both mates.
                            polyA ... polyA sequence with the length equal to read length

clip3pAdapterMMp            0.1
    double(s): max proportion of mismatches for 3p adapter clipping for each mate.  If one value is given, it will be assumed the same for both mates.

clip3pAfterAdapterNbases    0
    int(s): number of bases to clip from 3p of each mate after the adapter clipping. If one value is given, it will be assumed the same for both mates.

clip5pNbases                 0
    int(s): number(s) of bases to clip from 5p of each mate. If one value is given, it will be assumed the same for both mates.

#####UnderDevelopment_begin : not supported - do not use   
clip5pAdapterSeq            -
    string(s): adapter sequences to clip from 5p of each mate, separated by space.

clip5pAdapterMMp            0.1
    double(s): max proportion of mismatches for 5p adapter clipping for each mate, separated by space

clip5pAfterAdapterNbases    0
    int(s): number of bases to clip from 5p of each mate after the adapter clipping, separated by space.
#####UnderDevelopment_end

### Limits
limitGenomeGenerateRAM               31000000000
    int>0: maximum available RAM (bytes) for genome generation

limitIObufferSize                    30000000 50000000
    int(s)>0: max available buffers size (bytes) for input/output, per thread

limitOutSAMoneReadBytes              100000
    int>0: max size of the SAM record (bytes) for one read. Recommended value: >(2*(LengthMate1+LengthMate2+100)*outFilterMultimapNmax

limitOutSJoneRead                    1000
    int>0: max number of junctions for one read (including all multi-mappers)

limitOutSJcollapsed                  1000000
    int>0: max number of collapsed junctions

limitBAMsortRAM                         0
    int>=0: maximum available RAM (bytes) for sorting BAM. If =0, it will be set to the genome index size. 0 value can only be used with --genomeLoad NoSharedMemory option.

limitSjdbInsertNsj                     1000000
    int>=0: maximum number of junctions to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run

limitNreadsSoft                        -1
    int: soft limit on the number of reads

### Output: general
outFileNamePrefix               ./
    string: output files name prefix (including full or relative path). Can only be defined on the command line.

outTmpDir                       -
    string: path to a directory that will be used as temporary by STAR. All contents of this directory will be removed!
                                - ... the temp directory will default to outFileNamePrefix_STARtmp

outTmpKeep                      None
    string: whether to keep the temporary files after STAR runs is finished
                                None ... remove all temporary files
                                All ... keep all files

outStd                          Log
    string: which output will be directed to stdout (standard out)
                                Log                    ... log messages
                                SAM                    ... alignments in SAM format (which normally are output to Aligned.out.sam file), normal standard output will go into Log.std.out
                                BAM_Unsorted           ... alignments in BAM format, unsorted. Requires --outSAMtype BAM Unsorted
                                BAM_SortedByCoordinate ... alignments in BAM format, sorted by coordinate. Requires --outSAMtype BAM SortedByCoordinate
                                BAM_Quant              ... alignments to transcriptome in BAM format, unsorted. Requires --quantMode TranscriptomeSAM

outReadsUnmapped                None
   string: output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s).
                                None    ... no output
                                Fastx   ... output in separate fasta/fastq files, Unmapped.out.mate1/2

outQSconversionAdd              0
   int: add this number to the quality score (e.g. to convert from Illumina to Sanger, use -31)

outMultimapperOrder             Old_2.4
    string: order of multimapping alignments in the output files
                                Old_2.4             ... quasi-random order used before 2.5.0
                                Random              ... random order of alignments for each multi-mapper. Read mates (pairs) are always adjacent, all alignment for each read stay together. This option will become default in the future releases.

### Output: SAM and BAM
outSAMtype                      SAM
    strings: type of SAM/BAM output
                                1st word:
                                BAM  ... output BAM without sorting
                                SAM  ... output SAM without sorting
                                None ... no SAM/BAM output
                                2nd, 3rd:
                                Unsorted           ... standard unsorted
                                SortedByCoordinate ... sorted by coordinate. This option will allocate extra memory for sorting which can be specified by --limitBAMsortRAM.

outSAMmode                      Full
    string: mode of SAM output
                                None ... no SAM output
                                Full ... full SAM output
                                NoQS ... full SAM but without quality scores

outSAMstrandField               None
    string: Cufflinks-like strand field flag
                                None        ... not used
                                intronMotif ... strand derived from the intron motif. This option changes the output alignments: reads with inconsistent and/or non-canonical introns are filtered out.

outSAMattributes                Standard
    string(s): a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order.
                                ***Presets:
                                None        ... no attributes
                                Standard    ... NH HI AS nM
                                All         ... NH HI AS nM NM MD jM jI MC ch                                                                    
                                ***Alignment:
                                NH          ... number of loci the reads maps to: =1 for unique mappers, >1 for multimappers. Standard SAM tag.
                                HI          ... multiple alignment index, starts with --outSAMattrIHstart (=1 by default). Standard SAM tag.
                                AS          ... local alignment score, +1/-1 for matches/mismateches, score* penalties for indels and gaps. For PE reads, total score for two mates. Stadnard SAM tag.
                                nM          ... number of mismatches. For PE reads, sum over two mates.
                                NM          ... edit distance to the reference (number of mismatched + inserted + deleted bases) for each mate. Standard SAM tag.
                                MD          ... string encoding mismatched and deleted reference bases (see standard SAM specifications). Standard SAM tag.
                                jM          ... intron motifs for all junctions (i.e. N in CIGAR): 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT. If splice junctions database is used, and a junction is annotated, 20 is added to its motif value.
                                jI          ... start and end of introns for all junctions (1-based).
                                XS          ... alignment strand according to --outSAMstrandField.
                                MC          ... mate's CIGAR string. Standard SAM tag.
                                ch          ... marks all segment of all chimeric alingments for --chimOutType WithinBAM output.
                                cN          ... number of bases clipped from the read ends: 5' and 3'
                                ***Variation:
                                vA          ... variant allele
                                vG          ... genomic coordinate of the variant overlapped by the read.
                                vW          ... 1 - alignment passes WASP filtering; 2,3,4,5,6,7 - alignment does not pass WASP filtering. Requires --waspOutputMode SAMtag.
                                ha          ... haplotype (1/2) when mapping to the diploid genome. Requires genome generated with --genomeTransformType Diploid .                               
                                ***STARsolo:
                                CR CY UR UY ... sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing.
                                GX GN       ... gene ID and gene name for unique-gene reads.
                                gx gn       ... gene IDs and gene names for unique- and multi-gene reads.
                                CB UB       ... error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires --outSAMtype BAM SortedByCoordinate.
                                sM          ... assessment of CB and UMI.
                                sS          ... sequence of the entire barcode (CB,UMI,adapter).
                                sQ          ... quality of the entire barcode.
                                sF          ... type of feature overlap and number of features for each alignment
                                ***Unsupported/undocumented:
                                rB          ... alignment block read/genomic coordinates.
                                vR          ... read coordinate of the variant.

outSAMattrIHstart               1
    int>=0:                     start value for the IH attribute. 0 may be required by some downstream software, such as Cufflinks or StringTie.

outSAMunmapped                  None
    string(s): output of unmapped reads in the SAM format
                                1st word:
                                None   ... no output
                                Within ... output unmapped reads within the main SAM file (i.e. Aligned.out.sam)
                                2nd word:
                                KeepPairs ... record unmapped mate for each alignment, and, in case of unsorted output, keep it adjacent to its mapped mate. Only affects multi-mapping reads.

outSAMorder                     Paired
    string: type of sorting for the SAM output
                                Paired: one mate after the other for all paired alignments
                                PairedKeepInputOrder: one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files

outSAMprimaryFlag        OneBestScore
    string: which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG
                                OneBestScore ... only one alignment with the best score is primary
                                AllBestScore ... all alignments with the best score are primary

outSAMreadID            Standard
    string: read ID record type
                                Standard ... first word (until space) from the FASTx read ID line, removing /1,/2 from the end
                                Number   ... read number (index) in the FASTx file

outSAMmapqUnique        255
    int: 0 to 255: the MAPQ value for unique mappers

outSAMflagOR           0
    int: 0 to 65535: sam FLAG will be bitwise OR'd with this value, i.e. FLAG=FLAG | outSAMflagOR. This is applied after all flags have been set by STAR, and after outSAMflagAND. Can be used to set specific bits that are not set otherwise.

outSAMflagAND           65535
    int: 0 to 65535: sam FLAG will be bitwise AND'd with this value, i.e. FLAG=FLAG & outSAMflagOR. This is applied after all flags have been set by STAR, but before outSAMflagOR. Can be used to unset specific bits that are not set otherwise.

outSAMattrRGline        -
    string(s): SAM/BAM read group line. The first word contains the read group identifier and must start with "ID:", e.g. --outSAMattrRGline ID:xxx CN:yy "DS:z z z".
            xxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted.
            Comma separated RG lines correspons to different (comma separated) input files in --readFilesIn. Commas have to be surrounded by spaces, e.g.
            --outSAMattrRGline ID:xxx , ID:zzz "DS:z z" , ID:yyy DS:yyyy

outSAMheaderHD          -
    strings: @HD (header) line of the SAM header

outSAMheaderPG          -
    strings: extra @PG (software) line of the SAM header (in addition to STAR)

outSAMheaderCommentFile -
    string: path to the file with @CO (comment) lines of the SAM header

outSAMfilter            None
    string(s): filter the output into main SAM/BAM files
                        KeepOnlyAddedReferences ... only keep the reads for which all alignments are to the extra reference sequences added with --genomeFastaFiles at the mapping stage.
                        KeepAllAddedReferences ...  keep all alignments to the extra reference sequences added with --genomeFastaFiles at the mapping stage.


outSAMmultNmax          -1
    int: max number of multiple alignments for a read that will be output to the SAM/BAM files. Note that if this value is not equal to -1, the top scoring alignment will be output first
                        -1 ... all alignments (up to --outFilterMultimapNmax) will be output

outSAMtlen              1
    int: calculation method for the TLEN field in the SAM/BAM files
                        1 ... leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate
                        2 ... leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends

outBAMcompression       1
    int: -1 to 10  BAM compression level, -1=default compression (6?), 0=no compression, 10=maximum compression

outBAMsortingThreadN    0
    int: >=0: number of threads for BAM sorting. 0 will default to min(6,--runThreadN).

outBAMsortingBinsN      50
    int: >0:  number of genome bins for coordinate-sorting

### BAM processing
bamRemoveDuplicatesType  -
    string: mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only
                        -                       ... no duplicate removal/marking
                        UniqueIdentical         ... mark all multimappers, and duplicate unique mappers. The coordinates, FLAG, CIGAR must be identical
                        UniqueIdenticalNotMulti  ... mark duplicate unique mappers but not multimappers.

bamRemoveDuplicatesMate2basesN   0
    int>0: number of bases from the 5' of mate 2 to use in collapsing (e.g. for RAMPAGE)

### Output Wiggle
outWigType          None
    string(s): type of signal output, e.g. "bedGraph" OR "bedGraph read1_5p". Requires sorted BAM: --outSAMtype BAM SortedByCoordinate .
                    1st word:
                    None       ... no signal output
                    bedGraph   ... bedGraph format
                    wiggle     ... wiggle format
                    2nd word:
                    read1_5p   ... signal from only 5' of the 1st read, useful for CAGE/RAMPAGE etc
                    read2      ... signal from only 2nd read

outWigStrand        Stranded
    string: strandedness of wiggle/bedGraph output
                    Stranded   ...  separate strands, str1 and str2
                    Unstranded ...  collapsed strands

outWigReferencesPrefix    -
    string: prefix matching reference names to include in the output wiggle file, e.g. "chr", default "-" - include all references

outWigNorm              RPM
    string: type of normalization for the signal
                        RPM    ... reads per million of mapped reads
                        None   ... no normalization, "raw" counts

### Output Filtering
outFilterType                   Normal
    string: type of filtering
                                Normal  ... standard filtering using only current alignment
                                BySJout ... keep only those reads that contain junctions that passed filtering into SJ.out.tab

outFilterMultimapScoreRange     1
    int: the score range below the maximum score for multimapping alignments

outFilterMultimapNmax           10
    int: maximum number of loci the read is allowed to map to. Alignments (all of them) will be output only if the read maps to no more loci than this value.
         Otherwise no alignments will be output, and the read will be counted as "mapped to too many loci" in the Log.final.out .

outFilterMismatchNmax           10
    int: alignment will be output only if it has no more mismatches than this value.

outFilterMismatchNoverLmax      0.3
    real: alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value.

outFilterMismatchNoverReadLmax  1.0
    real: alignment will be output only if its ratio of mismatches to *read* length is less than or equal to this value.


outFilterScoreMin               0
    int: alignment will be output only if its score is higher than or equal to this value.

outFilterScoreMinOverLread      0.66
    real: same as outFilterScoreMin, but normalized to read length (sum of mates' lengths for paired-end reads)

outFilterMatchNmin              0
    int: alignment will be output only if the number of matched bases is higher than or equal to this value.

outFilterMatchNminOverLread     0.66
    real: sam as outFilterMatchNmin, but normalized to the read length (sum of mates' lengths for paired-end reads).

outFilterIntronMotifs           None
    string: filter alignment using their motifs
                None                           ... no filtering
                RemoveNoncanonical             ... filter out alignments that contain non-canonical junctions
                RemoveNoncanonicalUnannotated  ... filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept.

outFilterIntronStrands          RemoveInconsistentStrands
    string: filter alignments
                RemoveInconsistentStrands      ... remove alignments that have junctions with inconsistent strands
                None                           ... no filtering

### Output splice junctions (SJ.out.tab)
outSJtype                       Standard
    string: type of splice junction output
                                Standard    ... standard SJ.out.tab output
                                None        ... no splice junction output

### Output Filtering: Splice Junctions
outSJfilterReads                All
    string: which reads to consider for collapsed splice junctions output
                                All     ... all reads, unique- and multi-mappers
                                Unique  ... uniquely mapping reads only

outSJfilterOverhangMin          30  12  12  12
    4 integers:    minimum overhang length for splice junctions on both sides for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif
                                does not apply to annotated junctions

outSJfilterCountUniqueMin       3   1   1   1
    4 integers: minimum uniquely mapping read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif
                                Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied
                                does not apply to annotated junctions

outSJfilterCountTotalMin     3   1   1   1
    4 integers: minimum total (multi-mapping+unique) read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif
                                Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied
                                does not apply to annotated junctions

outSJfilterDistToOtherSJmin     10  0   5   10
    4 integers>=0: minimum allowed distance to other junctions' donor/acceptor
                                does not apply to annotated junctions

outSJfilterIntronMaxVsReadN        50000 100000 200000
    N integers>=0: maximum gap allowed for junctions supported by 1,2,3,,,N reads
                                i.e. by default junctions supported by 1 read can have gaps <=50000b, by 2 reads: <=100000b, by 3 reads: <=200000. by >=4 reads any gap <=alignIntronMax
                                does not apply to annotated junctions

### Scoring
scoreGap                     0
    int: splice junction penalty (independent on intron motif)

scoreGapNoncan               -8
    int: non-canonical junction penalty (in addition to scoreGap)

scoreGapGCAG                 -4
    int: GC/AG and CT/GC junction penalty (in addition to scoreGap)

scoreGapATAC                 -8
    int: AT/AC  and GT/AT junction penalty  (in addition to scoreGap)

scoreGenomicLengthLog2scale   -0.25
    int: extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)

scoreDelOpen                 -2
    int: deletion open penalty

scoreDelBase                 -2
    int: deletion extension penalty per base (in addition to scoreDelOpen)

scoreInsOpen                 -2
    int: insertion open penalty

scoreInsBase                 -2
    int: insertion extension penalty per base (in addition to scoreInsOpen)

scoreStitchSJshift           1
    int: maximum score reduction while searching for SJ boundaries in the stitching step


### Alignments and Seeding

seedSearchStartLmax             50
    int>0: defines the search start point through the read - the read is split into pieces no longer than this value

seedSearchStartLmaxOverLread    1.0
    real: seedSearchStartLmax normalized to read length (sum of mates' lengths for paired-end reads)

seedSearchLmax       0
    int>=0: defines the maximum length of the seeds, if =0 seed length is not limited

seedMultimapNmax      10000
    int>0: only pieces that map fewer than this value are utilized in the stitching procedure

seedPerReadNmax       1000
    int>0: max number of seeds per read

seedPerWindowNmax     50
    int>0: max number of seeds per window

seedNoneLociPerWindow    10
    int>0: max number of one seed loci per window

seedSplitMin                12
    int>0: min length of the seed sequences split by Ns or mate gap

seedMapMin              5
    int>0: min length of seeds to be mapped

alignIntronMin              21
    int: minimum intron size, genomic gap is considered intron if its length>=alignIntronMin, otherwise it is considered Deletion

alignIntronMax              0
    int: maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins

alignMatesGapMax            0
    int: maximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins

alignSJoverhangMin          5
    int>0: minimum overhang (i.e. block size) for spliced alignments

alignSJstitchMismatchNmax   0 -1 0 0
    4*int>=0: maximum number of mismatches for stitching of the splice junctions (-1: no limit).
                            (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif.

alignSJDBoverhangMin        3
    int>0: minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments

alignSplicedMateMapLmin     0
    int>0: minimum mapped length for a read mate that is spliced

alignSplicedMateMapLminOverLmate 0.66
    real>0: alignSplicedMateMapLmin normalized to mate length

alignWindowsPerReadNmax     10000
    int>0: max number of windows per read

alignTranscriptsPerWindowNmax       100
    int>0: max number of transcripts per window

alignTranscriptsPerReadNmax               10000
    int>0: max number of different alignments per read to consider

alignEndsType           Local
    string: type of read ends alignment
                        Local             ... standard local alignment with soft-clipping allowed
                        EndToEnd          ... force end-to-end read alignment, do not soft-clip
                        Extend5pOfRead1   ... fully extend only the 5p of the read1, all other ends: local alignment
                        Extend5pOfReads12 ... fully extend only the 5p of the both read1 and read2, all other ends: local alignment

alignEndsProtrude       0    ConcordantPair
    int, string:        allow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate
                        1st word: int: maximum number of protrusion bases allowed
                        2nd word: string:
                                            ConcordantPair ... report alignments with non-zero protrusion as concordant pairs
                                            DiscordantPair ... report alignments with non-zero protrusion as discordant pairs

alignSoftClipAtReferenceEnds    Yes
    string: allow the soft-clipping of the alignments past the end of the chromosomes
                                Yes ... allow
                                No  ... prohibit, useful for compatibility with Cufflinks

alignInsertionFlush     None
    string: how to flush ambiguous insertion positions
                        None    ... insertions are not flushed
                        Right   ... insertions are flushed to the right

### Paired-End reads
peOverlapNbasesMin          0
    int>=0:             minimum number of overlapping bases to trigger mates merging and realignment. Specify >0 value to switch on the "merginf of overlapping mates" algorithm.

peOverlapMMp                0.01
    real, >=0 & <1:     maximum proportion of mismatched bases in the overlap area

### Windows, Anchors, Binning

winAnchorMultimapNmax           50
    int>0: max number of loci anchors are allowed to map to

winBinNbits                     16
    int>0: =log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins.

winAnchorDistNbins              9
    int>0: max number of bins between two anchors that allows aggregation of anchors into one window

winFlankNbins                   4
    int>0: log2(winFlank), where win Flank is the size of the left and right flanking regions for each window

winReadCoverageRelativeMin      0.5
    real>=0: minimum relative coverage of the read sequence by the seeds in a window, for STARlong algorithm only.

winReadCoverageBasesMin      0
    int>0: minimum number of bases covered by the seeds in a window , for STARlong algorithm only.

### Chimeric Alignments
chimOutType                 Junctions
    string(s): type of chimeric output
                            Junctions       ... Chimeric.out.junction
                            SeparateSAMold  ... output old SAM into separate Chimeric.out.sam file
                            WithinBAM       ... output into main aligned BAM files (Aligned.*.bam)
                            WithinBAM HardClip  ... (default) hard-clipping in the CIGAR for supplemental chimeric alignments (default if no 2nd word is present)
                            WithinBAM SoftClip  ... soft-clipping in the CIGAR for supplemental chimeric alignments

chimSegmentMin              0
    int>=0: minimum length of chimeric segment length, if ==0, no chimeric output

chimScoreMin                0
    int>=0: minimum total (summed) score of the chimeric segments

chimScoreDropMax            20
    int>=0: max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length

chimScoreSeparation         10
    int>=0: minimum difference (separation) between the best chimeric score and the next one

chimScoreJunctionNonGTAG    -1
    int: penalty for a non-GT/AG chimeric junction

chimJunctionOverhangMin     20
    int>=0: minimum overhang for a chimeric junction

chimSegmentReadGapMax       0
    int>=0: maximum gap in the read sequence between chimeric segments

chimFilter                  banGenomicN
    string(s): different filters for chimeric alignments
                            None ... no filtering
                            banGenomicN ... Ns are not allowed in the genome sequence around the chimeric junction

chimMainSegmentMultNmax        10
    int>=1: maximum number of multi-alignments for the main chimeric segment. =1 will prohibit multimapping main segments.

chimMultimapNmax                    0
    int>=0: maximum number of chimeric multi-alignments
                                0 ... use the old scheme for chimeric detection which only considered unique alignments

chimMultimapScoreRange          1
    int>=0: the score range for multi-mapping chimeras below the best chimeric score. Only works with --chimMultimapNmax > 1

chimNonchimScoreDropMin         20
    int>=0: to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be greater than this value

chimOutJunctionFormat           0
    int: formatting type for the Chimeric.out.junction file
                                0 ... no comment lines/headers
                                1 ... comment lines at the end of the file: command line and Nreads: total, unique/multi-mapping

### Quantification of Annotations
quantMode                   -
    string(s): types of quantification requested
                            -                ... none
                            TranscriptomeSAM ... output SAM/BAM alignments to transcriptome into a separate file
                            GeneCounts       ... count reads per gene

quantTranscriptomeBAMcompression    1
    int: -2 to 10  transcriptome BAM compression level
                            -2  ... no BAM output
                            -1  ... default compression (6?)
                             0  ... no compression
                             10 ... maximum compression

quantTranscriptomeSAMoutput BanSingleEnd_BanIndels_ExtendSoftclip
    string: alignment filtering for TranscriptomeSAM output
                            BanSingleEnd_BanIndels_ExtendSoftclip ... prohibit indels and single-end alignments, extend softclips - compatible with RSEM
                            BanSingleEnd               ... prohibit single-end alignments, allow indels and softclips
                            BanSingleEnd_ExtendSoftclip ... prohibit single-end alignments, extend softclips, allow indels


### 2-pass Mapping
twopassMode                 None
    string: 2-pass mapping mode.
                            None        ... 1-pass mapping
                            Basic       ... basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly

twopass1readsN              -1
    int: number of reads to process for the 1st step. Use very large number (or default -1) to map all reads in the first step.


### WASP parameters
waspOutputMode              None
    string: WASP allele-specific output type. This is re-implementation of the original WASP mappability filtering by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061–1063 (2015), https://www.nature.com/articles/nmeth.3582 .
                            SAMtag      ... add WASP tags to the alignments that pass WASP filtering

### STARsolo (single cell RNA-seq) parameters
soloType                    None
    string(s): type of single-cell RNA-seq
                            CB_UMI_Simple   ... (a.k.a. Droplet) one UMI and one Cell Barcode of fixed length in read2, e.g. Drop-seq and 10X Chromium.
                            CB_UMI_Complex  ... multiple Cell Barcodes of varying length, one UMI of fixed length and one adapter sequence of fixed length are allowed in read2 only (e.g. inDrop, ddSeq).
                            CB_samTagOut    ... output Cell Barcode as CR and/or CB SAm tag. No UMI counting. --readFilesIn cDNA_read1 [cDNA_read2 if paired-end] CellBarcode_read . Requires --outSAMtype BAM Unsorted [and/or SortedByCoordinate]
                            SmartSeq        ... Smart-seq: each cell in a separate FASTQ (paired- or single-end), barcodes are corresponding read-groups, no UMI sequences, alignments deduplicated according to alignment start and end (after extending soft-clipped bases)

soloCBtype                  Sequence
    string: cell barcode type
                            Sequence: cell barcode is a sequence (standard option)
                            String: cell barcode is an arbitrary string

soloCBwhitelist             -
    string(s): file(s) with whitelist(s) of cell barcodes. Only --soloType CB_UMI_Complex allows more than one whitelist file.
                            None            ... no whitelist: all cell barcodes are allowed

soloCBstart                 1
    int>0: cell barcode start base

soloCBlen                   16
    int>0: cell barcode length

soloUMIstart                17
    int>0: UMI start base

soloUMIlen                  10
    int>0: UMI length

soloBarcodeReadLength       1
    int: length of the barcode read
                            1   ... equal to sum of soloCBlen+soloUMIlen
                            0   ... not defined, do not check

soloBarcodeMate             0
    int: identifies which read mate contains the barcode (CB+UMI) sequence
                            0   ... barcode sequence is on separate read, which should always be the last file in the --readFilesIn listed
                            1   ... barcode sequence is a part of mate 1
                            2   ... barcode sequence is a part of mate 2

soloCBposition              -
    strings(s):             position of Cell Barcode(s) on the barcode read.
                            Presently only works with --soloType CB_UMI_Complex, and barcodes are assumed to be on Read2.
                            Format for each barcode: startAnchor_startPosition_endAnchor_endPosition
                            start(end)Anchor defines the Anchor Base for the CB: 0: read start; 1: read end; 2: adapter start; 3: adapter end
                            start(end)Position is the 0-based position with of the CB start(end) with respect to the Anchor Base
                            String for different barcodes are separated by space.
                            Example: inDrop (Zilionis et al, Nat. Protocols, 2017):
                            --soloCBposition  0_0_2_-1  3_1_3_8

soloUMIposition             -
    string:                  position of the UMI on the barcode read, same as soloCBposition
                            Example: inDrop (Zilionis et al, Nat. Protocols, 2017):
                            --soloCBposition  3_9_3_14

soloAdapterSequence         -
    string:                 adapter sequence to anchor barcodes. Only one adapter sequence is allowed.

soloAdapterMismatchesNmax   1
    int>0:                  maximum number of mismatches allowed in adapter sequence.

soloCBmatchWLtype           1MM_multi
    string:                 matching the Cell Barcodes to the WhiteList
                            Exact                           ... only exact matches allowed
                            1MM                             ... only one match in whitelist with 1 mismatched base allowed. Allowed CBs have to have at least one read with exact match.
                            1MM_multi                       ... multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches.
                                                                Allowed CBs have to have at least one read with exact match. This option matches best with CellRanger 2.2.0
                            1MM_multi_pseudocounts          ... same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes.
                            1MM_multi_Nbase_pseudocounts    ... same as 1MM_multi_pseudocounts, multimatching to WL is allowed for CBs with N-bases. This option matches best with CellRanger >= 3.0.0
                            EditDist_2                    ... allow up to edit distance of 3 fpr each of the barcodes. May include one deletion + one insertion. Only works with --soloType CB_UMI_Complex. Matches to multiple passlist barcdoes are not allowed. Similar to ParseBio Split-seq pipeline. 

soloInputSAMattrBarcodeSeq  -
    string(s):              when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode sequence (in proper order).
                            For instance, for 10X CellRanger or STARsolo BAMs, use --soloInputSAMattrBarcodeSeq CR UR .
                            This parameter is required when running STARsolo with input from SAM. 
    
soloInputSAMattrBarcodeQual  -
    string(s):              when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode qualities (in proper order).
                            For instance, for 10X CellRanger or STARsolo BAMs, use --soloInputSAMattrBarcodeQual CY UY .
                            If this parameter is '-' (default), the quality 'H' will be assigned to all bases.

soloStrand                  Forward
    string: strandedness of the solo libraries:
                            Unstranded  ... no strand information
                            Forward     ... read strand same as the original RNA molecule
                            Reverse     ... read strand opposite to the original RNA molecule

soloFeatures                Gene
    string(s): genomic features for which the UMI counts per Cell Barcode are collected
                            Gene            ... genes: reads match the gene transcript
                            SJ              ... splice junctions: reported in SJ.out.tab
                            GeneFull        ... full gene (pre-mRNA): count all reads overlapping genes' exons and introns
                            GeneFull_ExonOverIntron ... full gene (pre-mRNA): count all reads overlapping genes' exons and introns: prioritize 100% overlap with exons
                            GeneFull_Ex50pAS        ... full gene (pre-RNA): count all reads overlapping genes' exons and introns: prioritize >50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.

#####UnderDevelopment_begin : not supported - do not use
                            Transcript3p    ... quantification of transcript for 3' protocols
#####UnderDevelopment_end

soloMultiMappers            Unique
    string(s): counting method for reads mapping to multiple genes           
                            Unique     ... count only reads that map to unique genes
                            Uniform    ... uniformly distribute multi-genic UMIs to all genes
                            Rescue     ... distribute UMIs proportionally to unique+uniform counts (~ first iteration of EM)
                            PropUnique ... distribute UMIs proportionally to unique mappers, if present, and uniformly if not.
                            EM         ... multi-gene UMIs are distributed using Expectation Maximization algorithm

soloUMIdedup                1MM_All
    string(s):              type of UMI deduplication (collapsing) algorithm
                            1MM_All                     ... all UMIs with 1 mismatch distance to each other are collapsed (i.e. counted once).
                            1MM_Directional_UMItools    ... follows the "directional" method from the UMI-tools by Smith, Heger and Sudbery (Genome Research 2017).
                            1MM_Directional             ... same as 1MM_Directional_UMItools, but with more stringent criteria for duplicate UMIs
                            Exact                       ... only exactly matching UMIs are collapsed.
                            NoDedup                     ... no deduplication of UMIs, count all reads.
                            1MM_CR                      ... CellRanger2-4 algorithm for 1MM UMI collapsing.

soloUMIfiltering            -
    string(s):              type of UMI filtering (for reads uniquely mapping to genes)
                            -                  ... basic filtering: remove UMIs with N and homopolymers (similar to CellRanger 2.2.0).
                            MultiGeneUMI       ... basic + remove lower-count UMIs that map to more than one gene.
                            MultiGeneUMI_All   ... basic + remove all UMIs that map to more than one gene.
                            MultiGeneUMI_CR    ... basic + remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0 .
                                                   Only works with --soloUMIdedup 1MM_CR
                                                
soloOutFileNames            Solo.out/          features.tsv barcodes.tsv        matrix.mtx
    string(s):              file names for STARsolo output:
                            file_name_prefix   gene_names   barcode_sequences   cell_feature_count_matrix

soloCellFilter              CellRanger2.2 3000 0.99 10
    string(s):              cell filtering type and parameters
                            None            ... do not output filtered cells
                            TopCells        ... only report top cells by UMI count, followed by the exact number of cells
                            CellRanger2.2   ... simple filtering of CellRanger 2.2. 
                                                Can be followed by numbers: number of expected cells, robust maximum percentile for UMI count, maximum to minimum ratio for UMI count
                                                The harcoded values are from CellRanger: nExpectedCells=3000;  maxPercentile=0.99;  maxMinRatio=10
                            EmptyDrops_CR   ... EmptyDrops filtering in CellRanger flavor. Please cite the original EmptyDrops paper: A.T.L Lun et al, Genome Biology, 20, 63 (2019): https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1662-y
                                                Can be followed by 10 numeric parameters:  nExpectedCells   maxPercentile   maxMinRatio   indMin   indMax   umiMin   umiMinFracMedian   candMaxN   FDR   simN 
                                                The harcoded values are from CellRanger:             3000            0.99            10    45000    90000      500               0.01      20000  0.01  10000

soloOutFormatFeaturesGeneField3    "Gene Expression"
    string(s):                field 3 in the Gene features.tsv file. If "-", then no 3rd field is output.

soloCellReadStats           None
    string:                 Output reads statistics for each CB
                            Standard    ... standard output

#####UnderDevelopment_begin : not supported - do not use
soloClusterCBfile           -
    string:                 file containing the cluster information for cell barcodes, two columns: CB cluster_index. Only used with --soloFeatures Transcript3p
#####UnderDevelopment_end
