NAME

       tophat-recondition.py - post-processing of TopHat unmapped reads

DESCRIPTION

       usage: tophat-recondition.py [-h] [-l LOGFILE] [-m MAPPED_FILE] [-q]

       [-r RESULT_DIR] [-u UNMAPPED_FILE] [-v]
              tophat_result_dir

       Post-process  TopHat  unmapped reads. For detailed information on the issues this software
       corrects,         please         consult          the          software          homepage:
       https://github.com/cbrueffer/tophat-recondition

   positional arguments:
       tophat_result_dir
              directory containing TopHat mapped and unmapped read files.

   optional arguments:
       -h, --help
              show this help message and exit

       -l LOGFILE, --logfile LOGFILE
              log file (optional, (default: result_dir/tophatrecondition.log)

       -m MAPPED_FILE, --mapped-file MAPPED_FILE
              Name of the file containing mapped reads (default: accepted_hits.bam)

       -q, --quiet
              quiet mode, no console output

       -r RESULT_DIR, --result_dir RESULT_DIR
              directory to write unmapped_fixup.bam to (default: tophat_output_dir)

       -u UNMAPPED_FILE, --unmapped-file UNMAPPED_FILE
              Name of the file containing unmapped reads (default: unmapped.bam)

       -v, --version
              show program's version number and exit