Question: hs37d5 samtools idxstats
0
gravatar for IRECG
8 months ago by
IRECG0
IRECG0 wrote:

Hello, I am using samtools idxstats and I'd like to know what is hs37d5. Is that only the decoy sequences or the sum of reference genome + decoy sequences?

I mean, I have different BAM files and I want to have a measure of the "coverage" of each one, I thought about calculating the percentage of mapped reads (= #mapped reads รท sequence length) using samtools idxstats output. Can I use that or is not representative and should I use the #mapped reads from chr1-chrY?

Thanks!

samtools • 393 views
ADD COMMENTlink modified 8 months ago by Kevin Blighe32k • written 8 months ago by IRECG0
0
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe32k
Republic of Ireland
Kevin Blighe32k wrote:

Quite a few resources from reputable individuals (including our very own Devon) and companies on this:

That should firmly help to explain hs37d5.

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For 'coverage' metrics, you appear to be referring to depth of coverage, which would be better served by using BEDTools coverage or BEDTools genomecov. SAMtools idxstats will give a different type of information, i.e., number of reads aligning to each of your contigs, and is more used for gauging overall alignment metrics.

Kevin

ADD COMMENTlink written 8 months ago by Kevin Blighe32k

Thank you! I haven't done BEDtools genomecov or coverage because in both cases I need my BAM, but also another file : -g in the first case and -a in the second one. I guess that in both cases it must be my reference genome, am I right?

ADD REPLYlink written 8 months ago by IRECG0
1

Yes, take a look here, where even the developer of BEDTools has provide an answer: Bedtools genomecov to identify regions at any coverage

ADD REPLYlink written 8 months ago by Kevin Blighe32k
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