Question: Calculate mean mappability of genomic windows
gravatar for Irsan
6.2 years ago by
Irsan7.2k wrote:

I would like to calculate the mappability of 50 kb windows of Mus musculus assembly 9 (mm9). I downloaded the mappability with 100 bp reads from UCSC and created windows with bedtools makewindows -g myGenomeFile.txt -w 50000 > windows.bed

I cannot just calculate the mean mappability of all overlapping elements in the mappability track for each feature in the windows.bed file because the mappability windows from UCSC have different lenghts. I believe the UCSC binary bigWigAverageOverBed is specifically made for this job. However, I keep getting segmentation faults with this binary when I try it. I cannot find any solutions for this segmentation fault. What are my alternatives/options?

Many thanks in advance

genome • 2.0k views
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Irsan7.2k

Did you find a solution? I am getting this, too. Thanks.

ADD REPLYlink written 3.7 years ago by moxu460
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