parameter issue

[perl-xxp]

Could you please specifically explain the exact meaning of these two parameters:
--min-cov
--min-frac
And I also have the question about the barcode association, is the barcode unique to each CRS sequence, that is considering this situation:
CRS1-----barcode1
CRS2-----barcode1
CRS3-----barcode1
if barcode 1 should be filtered?

Thanks

[visze]

First Question:

--min-cov: A minimum number of same BC that map to the same oligo. Larger value gives more evidence to be correct. But can remove lot’s of BCs (depending on the complexity, sequencing depth and quality of sequencing). Recommended option is 3.

--min-frac: Minimum fraction of same BC that map to the same oligo. E.g. 0.7 means that at least 70% of the BC map to the same oligo. A larger value gives more evidence to be correct. But can remove lots of BCs (depending on the complexity, sequencing depth and quality of sequencing). Recommended option is 0.7.

Second question:

In your example barcode1 is assigned equally (one-time) to 3 CRS sequences each. This one is filtered out. If you have something like that it should be retained and assigned to CRS3:

CRS1-----barcode1
CRS2-----barcode1
CRS3-----barcode1
CRS3-----barcode1
CRS3-----barcode1
CRS3-----barcode1
CRS3-----barcode1
CRS3-----barcode1
CRS3-----barcode1
CRS3-----barcode1

min-coverage 8 for CRS3 and fraction is 0.8.

IMPORTANT NOTE: MPRAflow will not developed further! Please use MPRAsnakeflow for a more advanced pipeline with lots of improvements and fixes.