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Combining start and end barcodes
Ryan Wick edited this page Aug 28, 2018
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3 revisions
For the native barcoding kit, barcodes can be present on both the start and end of reads. This makes for a few possibilities: the start/end barcodes can agree or disagree and either might be absent. The starts of reads are much more likely to have a barcode (over 80%) than the ends of reads (more like 50%).
Deepbinner has a few different options for how to handle these cases:
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--require_either: This is the most lenient mode and the default behaviour. Reads will be binned if either the start or end has a barcode. If both have a barcode and they conflict, the read goes in the 'none' bin. -
--require_start: This mode is a bit stricter. Reads must have a barcode at their start but not necessarily at the end. -
--require_both: This is the strictest mode. Reads are only binned if there is a matching barcode on each end.
| Start barcode | End barcode | require_either |
require_start |
require_both |
|---|---|---|---|---|
| 5 | none | 5 | 5 | none |
| 9 | 9 | 9 | 9 | 9 |
| 9 | 7 | none | none | none |
| 8 | none | 8 | 8 | none |
| none | 3 | 3 | none | none |