Hi all,
Long time reader, first time poster.
I've been processing some RNASeq data where the RNA was isolated using a Clontech's SMART kit which selects polyA+ mRNA. This was done single end, and the reads were mapped using Tophat.
I find that many genes have significant numbers of reads in the introns which I thought would be suppressed due to polyA+ selection. I've attached an example which is a screen grab from Seqmonk. An example of the "problematic" area is marked in green.
It would be good to know what others think, and whether these reads should be used as a measure of expression, or whether it would be wiser to use only exonic reads.
I should also point out these were run on a HiSeq and multiplexed on the same lane.
Many thanks,
Sham
Long time reader, first time poster.
I've been processing some RNASeq data where the RNA was isolated using a Clontech's SMART kit which selects polyA+ mRNA. This was done single end, and the reads were mapped using Tophat.
I find that many genes have significant numbers of reads in the introns which I thought would be suppressed due to polyA+ selection. I've attached an example which is a screen grab from Seqmonk. An example of the "problematic" area is marked in green.
It would be good to know what others think, and whether these reads should be used as a measure of expression, or whether it would be wiser to use only exonic reads.
I should also point out these were run on a HiSeq and multiplexed on the same lane.
Many thanks,
Sham
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