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PriceLab / snapr

SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis
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BAM record error: found spliced alignment without XS attribute #5

Closed yanzhangusa closed 9 years ago

yanzhangusa commented 9 years ago

When I used bam file which generated by snapr for cufflinks, I got the following error: BAM record error: found spliced alignment without XS attribute. I did some research and found that was because of there is no strand tag in that bam file. Which parameter that I need to add in snapr to make snapr generate them? I knew tophat and star could generate it but BWA could not.

Thanks yan

yanzhangusa commented 9 years ago

could specify strand in cufflinks. No need for snapr to generate them.