We are doing RNA Seq on Illumina GAII, and are seeing a lot of variation in coverage, which doesn't look as though it's Poisson distributed. Our sample originated from an RNA virus, but also contains some host rRNA, and both are showing this variation in coverage.
There is some correlation of coverage depth with GC content, but it doesn't explain most of the variation. Do others see this kind of variability of coverage?
We have hypothesised that secondary structure and amplification artefacts would explain some of the variation, but has anyone seen any research explaining variation in depth of coverage of RNA-Seq?
I've looked but haven't found anything remotely conclusive.
There is some correlation of coverage depth with GC content, but it doesn't explain most of the variation. Do others see this kind of variability of coverage?
We have hypothesised that secondary structure and amplification artefacts would explain some of the variation, but has anyone seen any research explaining variation in depth of coverage of RNA-Seq?
I've looked but haven't found anything remotely conclusive.
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