Hi,
When using the Whole Transcriptome protocol on total RNA (ie not poly-A+) with random priming of RT, have others noticed the frequent mismatches with reference sequence close to the ends of the reads (see attached image for example)? These are presumably due to the random mers used to prime the RT? How long are those N-mers?
Also, if anyone reading has any thoughts on how to treat multiple exactly identical reads in RNA-seq (=count once if these are PCR artefacts), I have started a specific thread on this seemingly overlooked topic...
When using the Whole Transcriptome protocol on total RNA (ie not poly-A+) with random priming of RT, have others noticed the frequent mismatches with reference sequence close to the ends of the reads (see attached image for example)? These are presumably due to the random mers used to prime the RT? How long are those N-mers?
Also, if anyone reading has any thoughts on how to treat multiple exactly identical reads in RNA-seq (=count once if these are PCR artefacts), I have started a specific thread on this seemingly overlooked topic...
Comment