Find out if you have amplicon reads.

hr3y · 01-07-2018, 10:01 PM

Is there really no way (program, tool) to tell if your BAM files have amplicon reads?

How is everyone doing it? determining a priori and using different analysis pipelines? or is this done by visually judging FastQC reports?

Any comments are welcome, I simply cannot believe we have no way to automatically tell if the reads are amplicons by library design; like, you would probably expect a really smaller number of equal start-end positions for PCR duplicates than amplicons, right? or at least less positions with duplicates in the case of PCR duplicates?

Anyway, thanks if anyone has any input!

cheers!

H.

hr3y · 01-07-2018, 11:09 PM

Possibly running This tool and make decisions from there?

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01-07-2018, 10:01 PM	#1
hr3y Junior Member Location: MX Join Date: May 2017 Posts: 7	Find out if you have amplicon reads. Is there really no way (program, tool) to tell if your BAM files have amplicon reads? How is everyone doing it? determining a priori and using different analysis pipelines? or is this done by visually judging FastQC reports? Any comments are welcome, I simply cannot believe we have no way to automatically tell if the reads are amplicons by library design; like, you would probably expect a really smaller number of equal start-end positions for PCR duplicates than amplicons, right? or at least less positions with duplicates in the case of PCR duplicates? Anyway, thanks if anyone has any input! cheers! H.

01-07-2018, 11:09 PM	#2
hr3y Junior Member Location: MX Join Date: May 2017 Posts: 7	EstimateLibraryComplexity Possibly running This tool and make decisions from there?