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fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
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Separate undetermined reads by lane in Fastq generation step #913

Closed pjbriggs closed 7 months ago

pjbriggs commented 7 months ago

Proposal to keep the undetermined reads separate by lane in the initial Fastq generation (make_fastqs), even if --no-lane-splitting is being used to merge assigned reads across lanes.

The purpose would be to enable better diagnostics from the downstream QC (run_qc) for the undetermined reads, to isolate lane effects which might otherwise be masked or more difficult to interpret (e.g. identifying contamination which only appears in a subset of lanes).

pjbriggs commented 7 months ago

The underlying issue (i.e. getting per-lane QC metrics for undetermined Fastqs) has been addressed in PR #916.