bigWigAverageOverBed

[Håvard Aanes]

Hi,

I'm using the bigWigAverageOverBed to calculate conservation scores of intervals in a bed file. I added the -minMax option. Is the min and max calculated for a specific sub-region of n bp's or is just the lowest and highest tile in the region, which can be variable?

It would be a nice and useful feature if it was possible to enter a specific  subset value and extract the max and min from these; say you have ~1000 bp intervals, and then you want to know the maximum found of every 10 bp tile within this region.

Thanks,

Håvard

[Luvina Guruvadoo]

Hello Havard,

Thank you for your question. For each item in a BED file, the program reports the highest and lowest scores that were found in the boundaries of the BED item. However, if you are looking for maxima from overlapping tiles, if this is what you mean by "the maximum found of every 10 bp tile within this region", then you can use the -samplAroundCenter option. The sampleAroundCenter=N option takes a sample of N bases around the center of each BED item. To do this, your BED file should contain one entry for each position like so:

chr17  1 2
chr17 2 3
chr17 3 4
chr17 4 5

Use -sampleAroundCenter=10. Note, it is integer arithmetic, so fractions are truncated (4.5 is turned into 4).

Alternatively, you may be interested in bwtools from Andy Pohl which can manage any kind of intersection with bigWig files:
https://github.com/CRG-Barcelona/bwtool

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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