Hi everyone, I'm pretty new to Nextflow and specifically the riboseq analysis. Had a question regarding the test_full profile: Is there a reason this test_full contains the additional hg38-mature-tRNAs-dna.fasta but in the default pipeline it does not? Is it conventional to remove tRNAs as well?
Some of my human cells riboseq samples have up to 72% tRNAs (of SortMeRNA hits) that were detected via SortMeRNA, For this sample, 21.6% of total reads matched to SortMeRNA. 15.8% of reads matched to silva-euk-28s.
Another question is why I only see <25% contaminants regardless of including tRNA or not--I did perform size exclusion gel extraction from 16-36nt, but I did not perform any rRNA depletion--should I not expect closer to 50-70% rRNA/contaminants?