Hello,
I hopefully have found most of the threads regarding duplicate removal in this forum.
(e.g. http://seqanswers.com/forums/showthr...uplicate+reads)
I am wondering if anyone has some input regarding this topic on small RNA data sets - how large an effect (if any) does real PCR duplicates have on real sRNA reads?
An sRNA read distribution profile typically displays many reads originating from an exact 5' position, which can be observed as 'hotspots' of read stacks across a reference.
I am analyzing miRNA/siRNA distribution profiles on viral genomes and hpRNAs, so the read depth is typically very high in very localized hotspots, but I am wondering if duplicates should be considered in my analysis, and if so, how does one distinguish real from duplicates reads?
thanks
I hopefully have found most of the threads regarding duplicate removal in this forum.
(e.g. http://seqanswers.com/forums/showthr...uplicate+reads)
I am wondering if anyone has some input regarding this topic on small RNA data sets - how large an effect (if any) does real PCR duplicates have on real sRNA reads?
An sRNA read distribution profile typically displays many reads originating from an exact 5' position, which can be observed as 'hotspots' of read stacks across a reference.
I am analyzing miRNA/siRNA distribution profiles on viral genomes and hpRNAs, so the read depth is typically very high in very localized hotspots, but I am wondering if duplicates should be considered in my analysis, and if so, how does one distinguish real from duplicates reads?
thanks
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