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EPPIcenter / mad4hatter

https://eppicenter.github.io/mad4hatter/
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use correct key in cutadapt json report for reporting number of ampli… #144

Closed bgpalmer closed 5 months ago

bgpalmer commented 5 months ago

…cons for sample_coverage.txt

bgpalmer commented 5 months ago

closing because read1_adapters is not providing counts we are expecting. a more manual approach is needed to get the true adapter counts. specifically, the recorded count includes reads that were filtered out for being too short. They seem to be included anyways because the primer was detected

kathryn1995 commented 5 months ago

I figured it out. To get the number to output we need to set --discard-untrimmed. Then the total is the right value in the cutadapt json file. However, you can't set --discard-untrimmed and --untrimmed-output at the same time. So we would have to decide between wanting the numbers from the json file or wanting it to output a file containing the reads that didn't have adapters (this file doesn't include anything filtered because the length was too short)