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Old 01-07-2018, 09:01 PM   #1
hr3y
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Location: MX

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Question 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.
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Old 01-07-2018, 10:09 PM   #2
hr3y
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Lightbulb EstimateLibraryComplexity

Possibly running This tool and make decisions from there?

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amplicon sequencing, bam files, haloplex, pcr duplicates, pipeline automation

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