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Old 09-28-2011, 10:31 AM   #1
biznatch
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Default Combine multiple wigs into one bigwig

I've got fixed step .wig files, 1 per chromosome, and I want to combine them into one bigwig file. I was going to concatenate them then use wigtobigwig. Step 2 of the instructions for creating a bigwig file says "Remove any existing 'track' or 'browser' lines from your wig file so that it contains only data." If I remove all the track lines then how will the wigtobigwig program know which data is on which chromosome? If I combine all my wig files then remove all the track lines it'll just be a file with a single column of numbers and no references to chromosomes. I think I'm missing something here...

Edit: I think I found the answer, someone else asking the same thing, I think the UCSC instructions need to be a bit clearer as even the UCSC "tech support" person was a little mixed up at first: https://lists.soe.ucsc.edu/pipermail...er/027040.html

Last edited by biznatch; 09-28-2011 at 12:40 PM.
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Old 08-25-2014, 12:27 AM   #2
Orr Shomroni
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Default

Personally, I'm using multiBamCov (a command in Bedtools) which converts multiple BAM files into BED, and piping it directly into wigToBigWig. This works since BED and WIG are of very similar format
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