lncRNA identification from RNAseq data
Hello,
I have some Zea mays rna data that I have analised for Differentially expressed genes, aligned with HISAT2,stingtie etc
Now I am interested in identifiying lncRNA sequences out of all the transcripts aligned. My data was polyA enriched, so it´ll be biased but I think it might be interesting to see the result.
Any tips on how to extract the lncRNA out of all the transcripts aligned? I believe that with stringtie files and gffcompare would be possible to extract the lncRNAs but I´m not sure where to start.
Any help is appreciated. Many thanks, Felipe
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pipe_cvm2 •
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Do you want to identify novel non-coding RNAs or just pull out the lncs form existing annotations, so basically a GTF file?