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Old 04-23-2015, 06:48 AM   #3
tokikake
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Location: Germany

Join Date: Nov 2011
Posts: 24
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Hi bastian,

thank you for your fast answer!
The rRNA/tRNA reads were filtered via mapping against the reference (and not with sortMeRNA). But the tmRNA was a good point. I added it to my annotations (so genes in general not only protein coding ones) and found up to 13% more reads mapping into genes. I try now to annotate the RNAs with rfam and infernal and hope to reduce the amount of outside mapped reads.
Nevertheless it is strange and I cannot see the same mapping bias in other projects, where I also didn't annotate the tmRNA (or any RNA prior to mapping, except tRNAs/rrNAs of course). Aber: Man lernt niemals aus!

Have anyone else ever tested the amount of mapped reads inside/outside genes? It would be interesting to know!
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