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BIC-seq2 for detecting CNVs in mouse mm10-mapped WGS data
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15 months ago
Russia, Moscow

Hi!

I'm interested in detecting copy number alterations in some mouse WGS data, specifically in locating regions of gene amplification and their boundaries. Never faced such a task before, so I googled it and BIC-seq / BIC-seq2 seems to be a good choice for a tool. However, as the manual states (http://compbio.med.harvard.edu/BIC-seq/), I would need mappability data to make a <configfile> in BIC-seq specific format. But UCSC table browser doesn't contain mappability track neither for mm10 nor for hg38 (which I checked just in case). There are mappability tracks for older versions like mm9 or hg19, but right now changing a genome version is not an option for me. So, my questions are: 1) Is BIC-Seq2 a good choice for such a task? 2) Is there any other source I should check for mm10 and hg38 mappability track? 3) My other ideas are either lifting it from mm9 to mm10 or building it from scratch, does it sound like something sensible to do? If I'm about to build it on my own, are there any goods tools for such task?

Thanks!

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