Dear all,
I am working with RNA data sequenced on the Hiseq4000 sequencer. I am trying to quantify the number of "optical duplicates" or "clustering duplicates". These duplicates appear when reads in nearby wells result from secondary exAmp seeding from a primary well when concentrations are sub-optimal.
I used MarkDuplicates (Picard 2.1.1) and followed this procedure : http://gatkforums.broadinstitute.org...swithmatecigar
But each time, MarkDuplicates find "0 optical duplicate clusters"...
I tested two alignement tools: TopHat and BWA, but each time, MarkDuplicates find no optical duplicate.
I tried on 96 samples.
Do you have any idea of why I cannot find any optical duplicate?
Thank you very much
I am working with RNA data sequenced on the Hiseq4000 sequencer. I am trying to quantify the number of "optical duplicates" or "clustering duplicates". These duplicates appear when reads in nearby wells result from secondary exAmp seeding from a primary well when concentrations are sub-optimal.
I used MarkDuplicates (Picard 2.1.1) and followed this procedure : http://gatkforums.broadinstitute.org...swithmatecigar
But each time, MarkDuplicates find "0 optical duplicate clusters"...
I tested two alignement tools: TopHat and BWA, but each time, MarkDuplicates find no optical duplicate.
I tried on 96 samples.
Do you have any idea of why I cannot find any optical duplicate?
Thank you very much
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