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.