visualizing interleaved QC data

[ycsong]

Hello,

I was wondering if it is possible to visualize an interleaved QC file using qfilterVis. We have some data that have gone through QC process using BBDuk/BBMap, similar to how JGI does the filtering.

From reading the tutorial, it appears that qfilterVis works with non-interleaved files (i.e., R1 and R2), unless I am missing something. Thank you in advance.

[franciscozorrilla]

Hey Young, sorry I missed this again, for some reason I dont get notified for new discussions.
Please feel free to tag me directly or open an issue so that I am notified in a timely manner.

Regarding your question, indeed the workflow is designed to work with non-interleaved reads, so it expects R1 and R2 files at the qfilter step. However, the qfilterVis rule will go through the additional .json statistics files generated by the qfiltering tool fastp, and then create a summary file for visualization qfiltering across samples. So if you want to use qfilterVis, you should have fastp output.

Hope this clarifies your question.
Best,
Francisco

[ycsong]

Thank you for the clarification, Francisco. Much appreciated.