Genome vs transcriptome alignement in STAR
1
0
Entering edit mode
3.0 years ago
roy.granit ▴ 880

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!

STAR RNA-Seq • 1.9k views
ADD COMMENT
1
Entering edit mode
3.0 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1209 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6