masked or unmasked genome reference for RNAseq

skly · 08-28-2015, 01:38 AM

Hi guys. I aligned RNAseq data to unmasked genome and hard masked genome, respectively. The mapping rate of the the former was about 92% and the latter rate was about 75%. It seemed that about 20% RNAseq data aligned to the repeating sequences of genome. So, which genome reference was better for RNAseq data, the unmasked genome or the hard masked?
Thanks a lot!

dpryan · 08-28-2015, 02:47 AM

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.

skly · 08-29-2015, 08:47 PM

Thanks dpryan~
I am clear.

Quote:

Originally Posted by dpryan

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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08-28-2015, 01:38 AM	#1
skly Junior Member Location: China Join Date: Jul 2010 Posts: 7	masked or unmasked genome reference for RNAseq Hi guys. I aligned RNAseq data to unmasked genome and hard masked genome, respectively. The mapping rate of the the former was about 92% and the latter rate was about 75%. It seemed that about 20% RNAseq data aligned to the repeating sequences of genome. So, which genome reference was better for RNAseq data, the unmasked genome or the hard masked? Thanks a lot!

08-28-2015, 02:47 AM	#2
dpryan 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.