Hi all,
I'm analysing some RNASeq results using the tophat–htseq–DESeq2 pipeline. The libraries were prepared using polyA selection and some of our samples had low RINs, so I was checking the data for evidence of 3′ bias. I used Qualimap 1.0's RNA-Seq QC tool to generate transcript coverage profiles for each of the samples, and bias is indeed evident in the samples that had low RINs. However, ALL the samples, including the ones with acceptable RINs, have a noticeable double peak in the coverage profile at 62.5–67.5 %.
I'm attaching a coverage plot from a sample with RIN of 7.5, one of the good ones. I'm curious whether anyone can explain the double peak or has observed it before.
Thanks,
Tom
PS the double peak looks a bit like batman to me...
I'm analysing some RNASeq results using the tophat–htseq–DESeq2 pipeline. The libraries were prepared using polyA selection and some of our samples had low RINs, so I was checking the data for evidence of 3′ bias. I used Qualimap 1.0's RNA-Seq QC tool to generate transcript coverage profiles for each of the samples, and bias is indeed evident in the samples that had low RINs. However, ALL the samples, including the ones with acceptable RINs, have a noticeable double peak in the coverage profile at 62.5–67.5 %.
I'm attaching a coverage plot from a sample with RIN of 7.5, one of the good ones. I'm curious whether anyone can explain the double peak or has observed it before.
Thanks,
Tom
PS the double peak looks a bit like batman to me...
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