Controlling error rate of substring within regular adapter
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- Dominant language
- Python
- Stars
- 587
- Forks
- 144
- Avg merge
- 2h 37m
- Merged PRs (30d)
- 1
Description
Is there a way to specify error tolerance for a specific subsequence within an adapter?
For example, in my regular 5' adapter, the first 8 nucleotides indicates the sample identity but the following 33 nts are shared across all samples. If I set a specific error tolerance (e.g. -e 6), I am afraid the errors might concentrate within the first 8 nts. I don't find anything I could use in the documentation or github issues that I can utilize, but hope to find out any clever tricks for this purpose. Thanks!
Is there a way to export what characters in the adapter sequence is matched in the output of --info-file ? Something like +++-+.+++ for a adapter with 9 nts, where + is a match, - is a mismatch, . is a deletion?
As I am requiring full match using min_overlap equal to length of adapter, if I get access to this field, then I can process the info file to filter out reads that has too many errors within the first 8 nucleotides.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No source file or test is named. Start by reviewing adapter matching and the --info-file behavior, including min_overlap and error tolerance. Done means the requested per-subsequence error control and match/mismatch/deletion information are supported or their limitations are clearly documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100