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Old 11-21-2019, 07:09 PM   #1
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Location: Greece

Join Date: Oct 2019
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Question 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
ndovro is offline   Reply With Quote

depth, idxstats, samtools

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