TopHat-Recondition : A post-processor for TopHat unmapped reads
Brueffer, Christian LU
and Saal, Lao H.
LU
(2016)
In BMC Bioinformatics
17(1).
- Abstract
Background: TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format - the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. Results: We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat. Conclusions:... (More)
Background: TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format - the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. Results: We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat. Conclusions: TopHat-Recondition can repair unmapped read files written by TopHat and is freely available under a 2-clause BSD license on GitHub: https://github.com/cbrueffer/tophat-recondition.
(Less)
- author
- Brueffer, Christian
LU
and Saal, Lao H.
LU
- organization
- publishing date
- 2016-05-04
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Deep sequencing, RNA-seq, Sequence alignment, Sequence analysis
- in
- BMC Bioinformatics
- volume
- 17
- issue
- 1
- article number
- 199
- publisher
- BioMed Central (BMC)
- external identifiers
-
- pmid:27142976
- wos:000375847500001
- scopus:84977539731
- ISSN
- 1471-2105
- DOI
- 10.1186/s12859-016-1058-x
- project
- RNA sequencing for molecular diagnostics in breast cancer
- language
- English
- LU publication?
- yes
- id
- 40961034-a7c5-4023-8f86-6c465616f292
- date added to LUP
- 2016-07-25 14:08:00
- date last changed
- 2025-03-08 13:44:40
@article{40961034-a7c5-4023-8f86-6c465616f292,
abstract = {{<p>Background: TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format - the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. Results: We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat. Conclusions: TopHat-Recondition can repair unmapped read files written by TopHat and is freely available under a 2-clause BSD license on GitHub: https://github.com/cbrueffer/tophat-recondition.</p>}},
author = {{Brueffer, Christian and Saal, Lao H.}},
issn = {{1471-2105}},
keywords = {{Deep sequencing; RNA-seq; Sequence alignment; Sequence analysis}},
language = {{eng}},
month = {{05}},
number = {{1}},
publisher = {{BioMed Central (BMC)}},
series = {{BMC Bioinformatics}},
title = {{TopHat-Recondition : A post-processor for TopHat unmapped reads}},
url = {{http://dx.doi.org/10.1186/s12859-016-1058-x}},
doi = {{10.1186/s12859-016-1058-x}},
volume = {{17}},
year = {{2016}},
}