I've done several Lib-A experiments where a significant percentage of my "A" reads are getting lost somewhere.
I know I have amplified template, since I get the corresponding "B" reads that should go with my missing A's, and I know the primers work for "A" sequencing.
I'm concerned that one of the runAnalysis filters is removing my reads, and I'd like to redo the signal processing to recover ALL keypass reads (i.e. turn off all quality filters) and see if my missing reads are there. Does anyone have experience in the correct filterTemplat.xml settings to do this?
I know I have amplified template, since I get the corresponding "B" reads that should go with my missing A's, and I know the primers work for "A" sequencing.
I'm concerned that one of the runAnalysis filters is removing my reads, and I'd like to redo the signal processing to recover ALL keypass reads (i.e. turn off all quality filters) and see if my missing reads are there. Does anyone have experience in the correct filterTemplat.xml settings to do this?
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