Subset of Transcripts- How do I proceed with it?
Hi!
I have run Stringtie with -e -B -G options and generated gene.abundance.tab and gtf files. How do I subset the transcripts? also I have a list of noncoding RNAs.
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Carlo Yague
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Varsha •
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Hello Varsha, can you please clarify your question ? On what criteria do you want to subset the transcripts ?