How important is the addXS step?

splicebox / PsiCLASS

Simultaneous multi-sample transcript assembler for RNA-seq data

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How important is the addXS step? #7

Closed sagnikbanerjee15 closed 4 years ago

sagnikbanerjee15 commented 4 years ago

Hello,

I was just wondering how important is the addXS step? This step is taking a very long time to finish so I was thinking about eliminating it. Please let me know how it would impact PsiCLASS.

Thank you.

mourisl commented 4 years ago

If there is no XS field in the bam, PsiCLASS won't be able to decide the strand of the read/intron, which is critical for the assembly. Most of the RNA-seq aligner will report the XS field by default. For STAR, there is an option "--outSAMstrandField" for this.

sagnikbanerjee15 commented 4 years ago

So if I configure STAR to output the XS field can I skip the addXS step?

mourisl commented 4 years ago

Yes, you can.

sagnikbanerjee15 commented 4 years ago

Great thanks!