marcelm / marcelm/cutadapt

Controlling error rate of substring within regular adapter

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Python
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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.

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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

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