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Improve/add UMI deduplication metrics #1277
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Since people complained about the poor performance, the generation of deduplication statistics if off by default now. You have to set the parameter |
Hi @MatthiasZepper, |
Apologies for stonewalling on this issue before. While hunting down the cause for issue #1303, it occurred to me that probably a botched MultiQC config is behind this issue as well. For some reason, we explicitly specify the MultiQC modules to be run and UMI-tools is nowhere to be found. Since we run MultiQC with a custom config outside the pipeline again, we did not notice. It should be fixed on this branch, but I struggle with testing at the moment. |
#1308 has been merged to |
Description of feature
Hello ^^
I'm having difficulties finding easy to understand stats on UMI deduplication in the outputs. It seems there is no section in the multiqc output, not even in the statistics table (where I would expect to have metrics about nb of reads before dedup, nb of reads after dedup, % duplication (from umi-tools dedup on alignements)).
In the output directory, I'm also not finding a log with easy to understand metrics from umi-tools dedup. I'm probably missing something.
Thanks in advance. Pierre
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