Hi, Question about counting multimapped reads, things like pirna and tRNA. For instance, I ran star aligning small rna mouse reads to mm10. Performed counting in htseq-count as well as in featurecounts using -M command, but still don't seem to get counts for these reads..just indication that I have a ton of non-unique alignments (expected given interest in tRNA). Any suggestions for counting trna/non unique reads? And quick simple question...how do I get ncrna features annotated in my counts.txt (e.g. miRNA, tRNA)? Only info in my output is ensembl number and chromosome.
Thanks a bunch, Greg
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