Strand attribute for Star alignments

[reetu]

Hi Alex,

I need strand information (XS attribute) for the alignment in order to get the downstream analysis working correctly for my pipeline. Is there any way in star to get this?

I have a mix of stranded and unstranded datasets. Does star needs any special parameters for stranded libs?

Thanks,

Reetu

[Alexander Dobin]

Hi Reetu,

for unstranded libraries, you can use --outSAMstrandField intronMotif option.

For stranded libraries, you would need to add the XS flag to the BAM file after mapping.

You can use this script from STAR distribution as an example of how to do it:

extras/scripts/tagXSstrandedData.awk

Cheers

Alex