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As a clinician I want high quality analysis, without false positive variant calls. At the moment in the UMI workflow we are not doing any quality or adapter-trimming. Not doing quality-trimming is ok as we are currently requiring at least 3 reads for error-correction which should reduce the need of quality-trimming. But the adapters may still have high quality and not be removed, and then be maintained and reduce the quality of downstream analysis. Therefore the adapters should be trimmed out.
Suggested approach
Probably add fastp adapter-trimming to the UMI workflow after concatenation, before UMI extraction, to also account for the possibility of adapter-dimers pushing the position of the UMI sequence further up the read.
Considered alternatives
No response
Deviation
No response
System requirements assessed
Yes, I have reviewed the system requirements
Requirements affected by this story
No response
Risk assessment needed
Needed
Not needed
Risk assessment
No response
SOUPs
No response
Can be closed when
No response
Blockers
No response
Anything else?
No response
The text was updated successfully, but these errors were encountered:
Here the UMI workflow is refactored to share the same upstream pre-processing as the TGA workflow (which will now use UMIs).
This means the following will be shared between the two workflows:
Concatenate reads
Trip adapters
Extract UMIs
Quality trim reads
Align reads with UMIs in read-header
Then they diverge into separate workflows where TGA only uses UMIs for dedup and the UMI-workflow requires minimum of 3,1,1 UMI-groups.
Need
As a clinician I want high quality analysis, without false positive variant calls. At the moment in the UMI workflow we are not doing any quality or adapter-trimming. Not doing quality-trimming is ok as we are currently requiring at least 3 reads for error-correction which should reduce the need of quality-trimming. But the adapters may still have high quality and not be removed, and then be maintained and reduce the quality of downstream analysis. Therefore the adapters should be trimmed out.
Suggested approach
Probably add fastp adapter-trimming to the UMI workflow after concatenation, before UMI extraction, to also account for the possibility of adapter-dimers pushing the position of the UMI sequence further up the read.
Considered alternatives
No response
Deviation
No response
System requirements assessed
Requirements affected by this story
No response
Risk assessment needed
Risk assessment
No response
SOUPs
No response
Can be closed when
No response
Blockers
No response
Anything else?
No response
The text was updated successfully, but these errors were encountered: