ncRNA (lincRNA) in ribodepleted RNAseq
I have a ribo-depleted RNA_sequenced data, In addition to mRNA seq I want to also study lincRNA in the same data. I have studied mRNA after aligning with HISAT. Now to study lincRNA, should I be aligning with HISAT or Star or it does not matter. In some papers I have seen Star being recommended while in others HISAT and cufflinks.
Any thoughts.
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Satyajeet Khare
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kanwarjag
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It should not matter. BTW, if by mRNA seq you mean polyA RNA seq, then quite a few non-coding RNA are polyadenylated. Also, quite a few mRNA are not polyadenylated and will be enriched in ribosome depleted samples.
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