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When providing lots of 5' anchored adapters with -e 2, an index can be generated and finding the adapters (barcodes) is fast. When then the maximum allowed number of errors is increased (say with -e 3), no index is generated (because an index is only generated up to two allowed errors), which has two consequences:
Matching becomes slow
Possibly ambiguous adapter/barcode assignments are no longer detected
We cannot always warn when no index can be created, but maybe when there are at least a certain number of anchored sequences and only the error rate is too high.
When providing lots of 5' anchored adapters with
-e 2
, an index can be generated and finding the adapters (barcodes) is fast. When then the maximum allowed number of errors is increased (say with-e 3
), no index is generated (because an index is only generated up to two allowed errors), which has two consequences:We cannot always warn when no index can be created, but maybe when there are at least a certain number of anchored sequences and only the error rate is too high.
CC @simonelsasser
CC @cnluzon
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