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Old 04-07-2009, 10:33 AM   #1
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Location: New York

Join Date: Mar 2009
Posts: 1
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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