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Old 05-05-2015, 05:23 AM   #1
Location: Norway

Join Date: Aug 2008
Posts: 35
Default Filter unique hits in Bowtie2 for stranded RNA-seq

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 ( suggested calculating the MAPQ score...

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Old 05-05-2015, 05:34 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

You appear to be using tophat2 rather than bowtie2, which is good given that you have RNAseq reads. In that case, just filter by MAPQ, namely those having MAPQ > 3 are "uniquely aligned"*.

*For one of the many definitions of that term.
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Old 05-05-2015, 06:37 AM   #3
Location: Norway

Join Date: Aug 2008
Posts: 35


That is correct, we are using TopHat2.

I have also been debating what 'uniquely' means, I guess it comes down to where you set a threshold
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