DOKK / manpages / debian 12 / tophat-recondition / tophat-recondition.1.en
TOPHAT-RECONDITION.PY(1) User Commands TOPHAT-RECONDITION.PY(1)

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

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

directory containing TopHat mapped and unmapped read files.

show this help message and exit
log file (optional, (default: result_dir/tophatrecondition.log)
Name of the file containing mapped reads (default: accepted_hits.bam)
quiet mode, no console output
directory to write unmapped_fixup.bam to (default: tophat_output_dir)
Name of the file containing unmapped reads (default: unmapped.bam)
show program's version number and exit
April 2019 tophat-recondition.py 1.4