Comments (4)
alexdobin
commented on June 25, 2024
This feature is high on my TODO list, hopefully will be added in the next month or so.
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dolittle007
commented on June 25, 2024
I have exactly the same problem. I am planning to make a RNA-seq pipeline using STAR-Stringtie-edgeR.
STAR is the best choice also due to GATK RNAseq pipeline is choosing STAR.
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alexdobin
commented on June 25, 2024
Hi @dolittle007
please do not comment on a closed issue, since I may not see it quickly enough.
Is your data unstranded or stranded?
For the unstranded data, you can use --outSAMstrandField intronMotif option to add the XS flag to all spliced alignments.
Cheers
Alex
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dolittle007
commented on June 25, 2024
I am handling stranded library. Stringtie doesn't allow the library type to be specified, and require "XS" tag no matter the strandness of reads is. So it forces me to use Cufflinks instead.
Thank you
Ting-You Wang
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Related Issues (20)
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