Title |
TopHat-Recondition: a post-processor for TopHat unmapped reads
|
---|---|
Published in |
BMC Bioinformatics, May 2016
|
DOI | 10.1186/s12859-016-1058-x |
Pubmed ID | |
Authors |
Christian Brueffer, Lao H. Saal |
Abstract |
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. 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. 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 . |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Sweden | 2 | 13% |
Germany | 1 | 7% |
Canada | 1 | 7% |
France | 1 | 7% |
China | 1 | 7% |
Unknown | 9 | 60% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 11 | 73% |
Members of the public | 4 | 27% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 2 | 5% |
Cuba | 1 | 2% |
Germany | 1 | 2% |
Denmark | 1 | 2% |
Sweden | 1 | 2% |
Unknown | 38 | 86% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 17 | 39% |
Student > Ph. D. Student | 10 | 23% |
Student > Bachelor | 6 | 14% |
Student > Master | 2 | 5% |
Student > Doctoral Student | 2 | 5% |
Other | 4 | 9% |
Unknown | 3 | 7% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 21 | 48% |
Biochemistry, Genetics and Molecular Biology | 10 | 23% |
Computer Science | 4 | 9% |
Engineering | 2 | 5% |
Medicine and Dentistry | 2 | 5% |
Other | 1 | 2% |
Unknown | 4 | 9% |