Comments (1)
@zztin I think you are probably right about the meaning of that code. Frankly, it's a weak criterion, but it should work for generating big-picture complexity results. It would not be a great approach if the purpose were, e.g., to accurately identify SNVs. It might lose information that would help at some important locus. Also, I've only ever considered how this should work for short reads.
Unfortunately I don't think I can answer your question now and I will leave this issue open, but here's one thing that might help: the best way to use Preseq is by providing a counts histogram (or the counts themselves). That would allow you to count duplicates according to your own definition.
I'll try go address this in more detail soon.
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Related Issues (20)
- `cmath` error on mac OS v11.3.1 HOT 4
- preseq sample reads is not all from bam?
- Histogram input file 0 counts HOT 4
- ERROR: reads unsorted in: HOT 3
- to-mr produces unexpected files with garbled reads
- ERROR: max count before zero is less than min required count (4) duplicates removed HOT 2
- lc_extrap error: saturation HOT 1
- ls_extrap: too many defects, negative CI, and causes HOT 3
- c_curve and lc_extrap output format
- preseq lc_extrap HOT 2
- lc_extrap: Segmentation dump HOT 1
- What are defects in approximation? What are the disadvantages to using defect mode? HOT 1
- Best practices with low-input library with high rate of PCR duplicates HOT 4
- ERROR: max count before zero is less than min required count (4) duplicates removed
- Errors During make HOT 7
- No configure file HOT 1
- ERROR: max count before zero is less than min required count (4) duplicates removed HOT 3
- about to-mr function HOT 1
- Using gc_extrap on mitochondrial target enrichment data HOT 3
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