bigWigSummary with bed file for a specific amount of datapoints in output

Question

[newscient]

Hi , I am trying to use the bigWigSummary tool from UCSC (https://genome.ucsc.edu/goldenpath/help/bigWig.html) which can extract summary information for your bigwig files. The functionality seems pretty straight forward :

bigWigSummary - Extract summary information from a bigWig file.
usage:
   bigWigSummary file.bigWig chrom start end dataPoints
Get summary data from bigWig for indicated region, broken into
dataPoints equal parts.  (Use dataPoints=1 for simple summary.)

NOTE:  start and end coordinates are in BED format (0-based)

options:
   -type=X where X is one of:
         mean - average value in region (default)
         min - minimum value in region
         max - maximum value in region
         std - standard deviation in region
         coverage - % of region that is covered
   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs

Nonetheless my command fails:

bigWigSummary -type=mean file.bed bigwig file.bed 500 > output

As i get it you can't run the tool for multiple chromosomes that are in the first column of my bed file. Anyone knows a work-around or a combination of tools that could give me average signal for some regions of interest (found in a bed file) but projected in a specific number of datapoints (e.g. 500 in my example) despite of the different lengths of the regions in the bed file?

Thanks in advance.

Answer 1

[Devon Ryan]

Have a look at computeMatrix scale-regions from deepTools.