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wososa / PSI-Sigma

PSI-Sigma
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STAR mapping parameters #3

Closed bling1000 closed 5 years ago

bling1000 commented 5 years ago

Hi, I'm trying using PSI-Sigma to do alternative splicing analysis. I already have mapped bam files generated by STAR without outFilterIntronMotifs options, is it (--outFilterIntronMotifs RemoveNoncanonical) necessary for the downstream analysis? I don't know whether I should rerun STAR.

Best wishes, Ling

wososa commented 5 years ago

Hi Ling,

Sorry that I missed your question. No, you don’t have to rerun STAR. The RemoveNoncanonical commend is optional. I added it because STAR’s definition of canonical junction is broad.

Woody