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Old 01-19-2016, 08:35 PM   #1
sjb343
Junior Member
 
Location: Ithaca

Join Date: Jul 2014
Posts: 1
Default Chromosome sizes don't match

Hi,

I'm having a heck of a time finding the chromosome sizes for mm9 that match the mm9 Bowtie pre-built indexes on their website. I have ChIP-seq data aligned using Bowtie2 to mm9 and used Macs2 to call peaks generating bedgraph files. Now I'm trying to convert these to BigWig files using bedgraphtobigwig but the UCSC chromosome sizes are not matching up. I can't find any threads with this problem but I'm not sure what I'm doing wrong. Since I can't seem to find anything, my questions is, is there a way to extract the chromosome sizes from the available Bowtie mm9 pre-built indexes?

Thanks,
sj
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