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chrisamiller / copyCat

a parallel R package for detecting copy-number alterations from short sequencing reads
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non-human mappability annotation files #4

Closed hongenxu closed 8 years ago

hongenxu commented 8 years ago

Hi Chris,

I am working on non-human organism and interested to use readdepth to call SCNAs in tumors. Followed the suggestion at readdepth, I comes to copyCat package.

Following the template at https://xfer.genome.wustl.edu/gxfer1/project/cancer-genomics/copyCat/, I successfully created entrypoints, gaps, and GC content files. But for mappability file, I used GEM-library and created a mappability file. Can you share some steps for transforming GEM output to the files in https://xfer.genome.wustl.edu/gxfer1/project/cancer-genomics/copyCat/?

Thanks, Best regards, Hongen

hongenxu commented 8 years ago

Hi,

I found this link https://xfer.genome.wustl.edu/gxfer1/project/cancer-genomics/readDepth/index.html.