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Forum: Bioinformatics 04-07-2009, 10:33 AM
Replies: 3
Views: 2,070
Posted By hbbio
Question Masked or unmasked genome for ChIP-seq analysis?

Should I use the masked genome or not (chromFaMasked vs. chromFa; both from UCSC) to align my chIP-seq data? If it depends on the alignment programs? Thanks!
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