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Illumina / interop

C++ Library to parse Illumina InterOp files
http://illumina.github.io/interop/index.html
GNU General Public License v3.0
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Q: Q>=30 fraction per barcode (== library) per lane #266

Closed sklages closed 8 months ago

sklages commented 3 years ago

Currently I am compiling quite a lot of stats for some "demultiplexing / run report" (mainly) using the Python bindings .. However, I didn't find a way to get the %Q>=30 fraction per barcode (and per lane) ...

Any idea how to do this. I want to avoid to read files other than the run XMLs and InterOp ... (currently this could be deduced from Stats.json AFAICS) ..

ezralanglois commented 3 years ago

This is not currently apart of InterOp. Adding it has been under discussion recently, but I would next expect that to change any time in the next year.

sklages commented 3 years ago

oh, okay, that would be quite useful, as it may directly show issues with libraries "early" on demultiplexing level before running and evaluating any QC on the final fastq files .. so thumbs up for this one :+1:

sklages commented 3 years ago

@ezralanglois .. just to get you correctly: is that not part of the InterOp file specifications or is it just not part of the programming API / Python bindings?

Stats.json reports Yield and YieldQ30 for each sample/barcode. Where has this been deduced from?

ezralanglois commented 3 years ago

It is not apart of the InterOp file specification. There is some discussion about whether this should be supported by InterOp given that every other metric comes from RTA, whereas this comes from bclconvert/bcl2fastq

sklages commented 3 years ago

I guess this is the same for the "undetermined indices" metrics (seqs, counts)? Coming from bcl-convert/bcl2fastq and written to some textual output files (Top_Unknown_Barcodes.csv/Stats.json)..?

ezralanglois commented 3 years ago

Yup, same for that.

ezralanglois commented 8 months ago

No plan to support this in InterOp. I believe bclconvert will deprecate writing out the InterOp file