Mappability Scores from bigWigAverageOverBed all zero

Question

[eric.kern13]

Hi Biostars,

I'm using UCSC's bigWigAverageOverBed tool to find the average mappability scores for some regions in chromosome 22. The result is nothing but zeroes. I assume this is incorrect. Can you figure out why and help me solve this issue? Some details:

As input, I am using the 50-mer file from http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability, which is a good-sized binary file as I expected. I also use (as the second argument) a BED file I made that looks like this:

22    16084594    16084644    0
22    16084644    16084694    1
22    16084694    16084744    2
22    16084744    16084794    3
22    16084794    16084834    4
22    16100468    16100518    5
22    16100518    16100568    6

The result is a tab-separated file with nothing but the region indices (standing for names), their lengths, and some zeroes:

1       50      0       0       0       0
2       50      0       0       0       0
3       50      0       0       0       0
4       40      0       0       0       0
5       50      0       0       0       0
6       50      0       0       0       0

Thanks!

Answer 1

[eric.kern13]

I solved this issue by switching to the bigWigSummary tool and writing 'chr22' in place of '22'.

[eric.kern13]

This is the second time I've had this problem, and it makes me want to chrY.