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Old 08-28-2015, 02:47 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Use the unmasked (or soft masked) genome. Actually, use that for everything that doesn't explicitly state that it wants a hard masked genome. There are MANY genes that overlap repeat regions, at least partially and you'll be missing alignments to them if you hard mask a genome. Similarly, there's often expression of some repeats (this is mostly just noise), and by using a hard masked genome you'll increase your false-positive alignment rate of sequence originated from such repeats.
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