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Discrepancy between samtools IDXSTATS and depth
Hi all,
i am baffled from some results and i was wondering if anyone can help.
I am doing RNAseq.
I got my sample, aligned it with STAR on a known reference and used samtools idxstats on the produced sortedbycoord file after indexing.
I get all my contigs/chroms and then run samtools depth for each one of them with -aa.
For some, even though idxstats reports a handful of mapped reads, I get 0 for all the bps with depth.
What am i missing?
Thanks for your time
i am baffled from some results and i was wondering if anyone can help.
I am doing RNAseq.
I got my sample, aligned it with STAR on a known reference and used samtools idxstats on the produced sortedbycoord file after indexing.
I get all my contigs/chroms and then run samtools depth for each one of them with -aa.
For some, even though idxstats reports a handful of mapped reads, I get 0 for all the bps with depth.
What am i missing?
Thanks for your time
