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GenomiqueENS / toulligQC

A post sequencing QC tool for Oxford Nanopore sequencers
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Barcodes in dorado output #22

Closed phpeters closed 8 months ago

phpeters commented 8 months ago

Hej,

Thanks for this really pretty tool! I encountered a small issue when using it with dorado's output:

a) When demultiplexing with dorado demux, toulligQC (v2.6) does not produce the barcode plots. This is due to the sequencing_summary_extractor.py which recognized the column "barcode_arrangement" but dorado's column name is only "barcode". I used dorado v0.5.1 and provided the barcodes via sample-sheet and demultiplexing kit (dorado basecaller ${basecallmodel} pod5/ --sample-sheet ${sampleSheet} $demuxKit ). When I changed my sequencing_summary.txt column to "barcode_arrangement", toulligQC produced the plots properly.

b) Is it possible to skip/modify the barcode-name check in toulligqc.py (ctrl+F: "Get barcode selection")? I'm have our lab's (integer) sampleID's as barcode names in the sequeuncing_summary and would have to add "BC" or "barcode" as prefix such that I don't et the error "ERROR: No known barcode found in provided list of barcodes". In dorado, you can specify now your own custom barcode sets as well with different names. That would be cool to be changed in toulligQC!

Thanks a ton and have a great week! Philipp

alihamraoui commented 8 months ago

Hej @phpeters,

Thank you for the great suggestions; they contribute to improving ToulligQC.

I addressed points (a) and (b) in commits 055b15e352d043974f597a5652697ec91a28cb00 and c387d9c2a83982eafc3acbbd7b5a44c51ffb471e.

These changes will be deployed in the next version of ToulligQC, coming soon.

Thanks again! Ali

phpeters commented 8 months ago

Merci for the quick fix, Ali! I'll try it out soon. All the best! Philipp