tophat-recondition1
Post-processing of tophat unmapped reads
Overview
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
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).