ncRNA (lincRNA) in ribodepleted RNAseq

Question

[kanwarjag]

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.

Answer 1

[Satyajeet Khare]

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.

Best,