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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.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Deep sequencing, RNA-seq, Sequence alignment, Sequence analysis
in
BMC Bioinformatics
volume
17
issue
1
publisher
BioMed Central
external identifiers
  • Scopus:84977539731
ISSN
1471-2105
DOI
10.1186/s12859-016-1058-x
language
English
LU publication?
yes
id
40961034-a7c5-4023-8f86-6c465616f292
date added to LUP
2016-07-25 14:08:00
date last changed
2016-09-20 03:04:05
@misc{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},
  keyword      = {Deep sequencing,RNA-seq,Sequence alignment,Sequence analysis},
  language     = {eng},
  month        = {05},
  number       = {1},
  publisher    = {ARRAY(0xa1c5fa0)},
  series       = {BMC Bioinformatics},
  title        = {TopHat-Recondition : A post-processor for TopHat unmapped reads},
  url          = {http://dx.doi.org/10.1186/s12859-016-1058-x},
  volume       = {17},
  year         = {2016},
}