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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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how to get % >=q30, % PhiX aligned and % demultiplexed at library level #253

Closed yelekley closed 3 years ago

yelekley commented 3 years ago

Hello, I would like to get % >=q30, % PhiX aligned and % demultiplexed at library level. I'm able to get these stats at 'lane' and 'read' level but wondering how to get these at library level.

I need to get % of >= Q30 Bases (PF) and %PhiX aligned per sample_id for QA monitoring. % of >= Q30 is listed in Demultiplex_Stats.htm, however, it would be nice to avoid parsing the file and just use an InterOp library. Could you please let me know if it's possible or not? If not possible, I will parse the htm file.

Thanks

ezralanglois commented 3 years ago

The InterOp library does provide this functionality. You cannot get % PhiX aligned per sample because PhiX is not indexed. We don't have % >=Q30 per sample either. You can use FastQC to get that information. % Demux can be obtained from the output of the bcl conversion program.