```
umi_tools prepare-for-rsem --help
```

prepare_for_rsem - make output from dedup or group compatible with RSEM

Usage: umi_tools prepare_for_rsem [OPTIONS] [--stdin=IN_BAM] [--stdout=OUT_BAM]

       note: If --stdout is ommited, standard out is output. To
             generate a valid BAM file on standard out, please
             redirect log with --log=LOGFILE or --log2stderr 

For full UMI-tools documentation, see https://umi-tools.readthedocs.io/en/latest/

Options:
  --version             show program's version number and exit

  RSEM preparation specific options:
    --tags=TAGS         Comma-seperated list of tags to transfer from read1 to
                        read2
    --sam               input and output SAM rather than BAM

  input/output options:
    -I FILE, --stdin=FILE
                        file to read stdin from [default = stdin].
    -L FILE, --log=FILE
                        file with logging information [default = stdout].
    -E FILE, --error=FILE
                        file with error information [default = stderr].
    -S FILE, --stdout=FILE
                        file where output is to go [default = stdout].
    --temp-dir=FILE     Directory for temporary files. If not set, the bash
                        environmental variable TMPDIR is used[default = None].
    --log2stderr        send logging information to stderr [default = False].
    --compresslevel=COMPRESSLEVEL
                        Level of Gzip compression to use. Default (6)
                        matchesGNU gzip rather than python gzip default (which
                        is 9)

  profiling options:
    --timeit=TIMEIT_FILE
                        store timeing information in file [none].
    --timeit-name=TIMEIT_NAME
                        name in timing file for this class of jobs [all].
    --timeit-header     add header for timing information [none].

  common options:
    -v LOGLEVEL, --verbose=LOGLEVEL
                        loglevel [1]. The higher, the more output.
    -h, --help          output short help (command line options only).
    --help-extended     Output full documentation
    --random-seed=RANDOM_SEED
                        random seed to initialize number generator with
                        [none].