Hi All,
I mapped a mouse DNA sequence data to mouse genome mm10 and want to calculate mappability. Are there any tools or proper way to do this? Thank you in advance.
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written
by
charlesberkn •
I assume you generated reads that should evenly cover the genome. In that case, "samtools depth" with awk will allow you to get a proper mappability track.
Yes, my reads cover the genome. Could you please tell me more detail about how to do it or where you know I can find a calculation example? I am new in the field. Thank you.
Sure, let's assume that you generated reads with 50x coverage of the genome (this is the 50 below). You could do something like:
samtools depth -aa some_alignment_file.bam | awk '{if($3>50){$3=50} printf("%s\t%i\t%i\t%f", $1,$2-1,$2,$3/50)}' > mappability.bedGraph
Note, however, that UCSC has mappability tracks for some organisms, so you might also check there.
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written
by
Devon Ryan
in this command 50 is windows size?
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