Genome vs transcriptome alignement in STAR

Question

[roy.granit]

Hi All,

I suspect that my sample might have dna contamination. Is there a way of telling the fraction of reads mapped to the transcriptome vs genome when using the STAR aligner?

I have used the --quantMode TranscriptomeSAM flag so I guess that can use samtools to count the number of reads mapped to the trascriptome

Thanks!

Answer 1

[grant.hovhannisyan]

If you used --quantMode GeneCounts, then in count file there will be N_noFeature, i.e. reads that were not assigned to any feature. It can be a proxy of how much "genomic" reads you have. However if you work a non-model organism it can be that these reads are coming from not yet annotated genes.