TOPHAT-RECONDITION.PY(1)

🎀 TOPHAT-RECONDITION.PY 🎀

okay bestie, gather round, because this is tophat-recondition.py from the User Commands section of your manual, and she is here to fix up your TopHat unmapped reads. no cap. 💖

✨ NAME ✨

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

🌸 DESCRIPTION 🌸

the usage vibe is literally this:

tophat-recondition.py [-h] [-l LOGFILE] [-m MAPPED_FILE] [-q]
                      [-r RESULT_DIR] [-u UNMAPPED_FILE] [-v]
                      tophat_result_dir

so what does she do? she post-processes TopHat unmapped reads. that's the whole gig. 💅

and if you want the detailed tea on which issues this software corrects, the homepage is right here, go read it, it's giving documentation:

https://github.com/cbrueffer/tophat-recondition

🌈 positional arguments

• tophat_result_dir — the directory that's holding your TopHat mapped and unmapped read files. she needs it. it's not optional. periodt.

💜 optional arguments

• -h, --help — shows this help message and then dips. classic. 👑
• -l LOGFILE, --logfile LOGFILE — the log file. it's optional, and the default is result_dir/tophatrecondition.log.
• -m MAPPED_FILE, --mapped-file MAPPED_FILE — the name of the file with your mapped reads in it. default is accepted_hits.bam.
• -q, --quiet — quiet mode, aka no console output. she's not talking. 🤫
• -r RESULT_DIR, --result_dir RESULT_DIR — the directory where unmapped_fixup.bam gets written. default is tophat_output_dir.
• -u UNMAPPED_FILE, --unmapped-file UNMAPPED_FILE — the name of the file with your unmapped reads in it. default is unmapped.bam.
• -v, --version — shows the program's version number and then exits. iconic behaviour. ✨

real talk though: the option is spelled --result_dir with an underscore, not a dash. do not come for me, that's just how she is. type it exactly like that or she will simply not know what you want. 💀

🦋 SEE ALSO 🦋

ngl there's nothing else listed here, so just go read the homepage again, iykyk: https://github.com/cbrueffer/tophat-recondition 🫶

and that's the whole page, bestie!! this was tophat-recondition.py 1.4, dated April 2019, living her best life in the User Commands section. go fix those reads. mwah. 💖✨🎀