---
name: "tophat-recondition"
section: "1"
platform: "linux"
package: "tophat-recondition"
version: "1.4-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/tophat-recondition"
---

# tophat-recondition(1)

post-processing of TopHat unmapped reads

## 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