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https://github.com/cbrueffer/tophat-recondition
Post-processor for TopHat unmapped.bam files making them usable by downstream software.
https://github.com/cbrueffer/tophat-recondition
bioinformatics ngs python sam tophat tophat-recondition
Last synced: 2 months ago
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Post-processor for TopHat unmapped.bam files making them usable by downstream software.
- Host: GitHub
- URL: https://github.com/cbrueffer/tophat-recondition
- Owner: cbrueffer
- License: bsd-2-clause
- Created: 2014-10-29T14:12:58.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2019-07-18T21:28:14.000Z (over 5 years ago)
- Last Synced: 2023-10-20T18:42:58.033Z (about 1 year ago)
- Topics: bioinformatics, ngs, python, sam, tophat, tophat-recondition
- Language: Python
- Homepage:
- Size: 56.6 KB
- Stars: 7
- Watchers: 5
- Forks: 5
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
- Citation: CITATION
Awesome Lists containing this project
README
TopHat-Recondition
==================
[](http://bioconda.github.io)
tophat-recondition is a post-processor for TopHat unmapped reads (contained in *unmapped.bam*), making them compatible with downstream tools
(e.g., the Picard suite, samtools, GATK) ([TopHat issue #17](https://github.com/DaehwanKimLab/tophat/issues/17)). It also works around bugs in TopHat:
- the "mate is unmapped" SAM flag is not set on any reads in the unmapped.bam file ([TopHat issue #3](https://github.com/DaehwanKimLab/tophat/issues/3))
- the mapped mate of an unmapped read can be absent from *accepted_hits.bam*, creating a mismatch between the file and the unmapped read's flags ([TopHat issue #16](https://github.com/DaehwanKimLab/tophat/issues/16))
This software was developed as part of a PhD research project in the
[laboratory of Lao H. Saal, Translational Oncogenomics Unit, Department of Oncology and Pathology, Lund University, Sweden](http://www.med.lu.se/saalgroup).
A detailed description of the software can be found in [Brueffer and Saal (2016)](http://dx.doi.org/10.1186/s12859-016-1058-x).
Requirements
------------
- Python 2.7 or Python 3
- [pysam](https://github.com/pysam-developers/pysam)
TopHat-Recondition is available for installation with the conda package manager via the [bioconda](http://bioconda.github.io/) channel: ```conda install -c bioconda tophat-recondition```
Usage
-----
```
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/tophat-
recondition.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
```
Please make sure *tophat_output_dir* contains both, the mapped file (default: *accepted_hits.bam*) and the unmapped file (default: *unmapped.bam*). The fixed
reads will be written to a file with the unmapped file name stem and the suffix *_fixup*, e.g. *unmapped_fixup.bam*, in *result_dir*.
**Note:** The unmapped file is read into memory, so make sure your computer has enough RAM to fit it.
Details
-------
Specifically, the script does the following (see [SAM format specification](http://samtools.github.io/hts-specs/SAMv1.pdf)
for details on the fields in capital letters):
- Fixes wrong flags resulting from a bug in TopHat:
* For paired reads where both reads are unmapped, TopHat does not set the 0x8 flag ("mate is unmapped") on either read.
- Removes /1 and /2 suffixes from read names (QNAME), if present.
- Sets mapping quality (MAPQ) for unmapped reads to 0. TopHat sets it to 255 which some downstream tools don't like (even though it is a valid value according to the SAM specification).
- If an unmapped read's paired read is mapped, set the following fields in the unmapped read (downstream tools like Picard AddOrReplaceReadGroups get confused by the values TopHat fills in for those fields):
* RNAME: RNAME of the paired read
* RNEXT: RNAME of the paired read
* POS: POS of the paired read
* PNEXT: 0
- For unmapped reads with missing mapped mates, unset the mate-related flags to effectively make them unpaired. The following flags are unset:
* 0x1 (mate is paired)
* 0x2 (mate in proper pair)
* 0x8 (mate is unmapped)
* 0x20 (mate is reversed)
* 0x40 (first in pair)
* 0x80 (second in pair)
Examples of error messages emitted by downstream tools when trying to process unmapped reads without some or all of these
modifications can be found in [this thread in the SEQanswers forum](http://seqanswers.com/forums/showthread.php?t=28155),
which lead to the development of this software.
Citation
--------
If you use this software in your research and would like to cite it, please use the citation information in the [CITATION](https://github.com/cbrueffer/tophat-recondition/blob/master/CITATION) file.