Reverses strandedness tags (XS) in BAM. Every XS:A:+ tag is changed to XS:A:- and vice versa.
Reverses strandedness tags (XS) in BAM. Every XS:A:+ tag is changed to XS:A:- and vice versa.
If you have stranded RNA-seq data and suspect that a wrong strandedness parameter value was used when aligning the reads to genome with HISAT2 or TopHat, you can correct the XS tags in the BAM file with this tool. XS tags are used by the Cuffdiff and Cufflinks tools when assembling transcripts. Note that the XS tags are not used by HTseq tools when counting reads per genes.
In most cases running this tool is faster than running a new alignment.
The analysis output consists of the following files:
This tool is based on the SAMtools package.
Please cite the article The Sequence alignment/map (SAM) format and SAMtools by Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) Bioinformatics, 25, 2078-9. [PMID: 19505943].