Extraction of BigWig data from UCSC

[Anexum]

Hi,
I have a set of big wig files for ChIP-seq data and im looking to extract the values over a set genomic interval. However I have over 170 different tracks to extract, and I was wondering if there was a way to do it as a batch process?

Any help is appreciated

[dpryan]

Either use bash with an appropriate UCSC tool or python with pyBigWig. Depending on what exactly you want to do, you could also use deepTools (it can handle remote files as well, though be sure to not use many threads in this case).

[Richard Finney]

Use your favorite language to generate a quick script: bash,perl, python, objective haskell, whatever. Learn one of these tools enough to smack around a list of files. There is no alternative to skinning your knees and learning. There is no iphone app. Make sure you are backed up.

Beg , borrow, steal, build the UCSC bigWigToWig program .... or just download it from here ....

http://hgdownload.cse.ucsc.edu/admin/exe/

make bigWigToWig executable. run it without arguments to see how to use it.

(dont need the chrom size files like you do for wigToBigWig)

So .... using the bash command line in this case ..... here's a real ugly hack ...

ls *.bw | awk '{print "/whereveritis/bigWigToBigWig -chrom=chr1 -start=1 -end-1000 "$1" out."$1".wig"}' | bash


Nota bene: there are other UCSC bigwig utilities you might check out.