Hi all,
We have PE stranded RNA-seq data, and we want to filter the alignment files for uniquely mapping reads (ie. no multi-hit reads).
We have done this before for 'unstranded' data based on the XS tag in the alignment file, however all I seem to get in the file now is:
XS:A:+ and XS:A:-
Any tips on how to filter multi-hit reads with stranded data? I saw that this thread (http://seqanswers.com/forums/showthread.php?t=39206) suggested calculating the MAPQ score...
Matt
We have PE stranded RNA-seq data, and we want to filter the alignment files for uniquely mapping reads (ie. no multi-hit reads).
We have done this before for 'unstranded' data based on the XS tag in the alignment file, however all I seem to get in the file now is:
XS:A:+ and XS:A:-
Any tips on how to filter multi-hit reads with stranded data? I saw that this thread (http://seqanswers.com/forums/showthread.php?t=39206) suggested calculating the MAPQ score...
Matt
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