table of contents
| TOPHAT-RECONDITION.PY(1) | User Commands | TOPHAT-RECONDITION.PY(1) |
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
| April 2019 | tophat-recondition.py 1.4 |