Output cut offsets in separate file
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- Dominant language
- Python
- Stars
- 587
- Forks
- 144
- Avg merge
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- Merged PRs (30d)
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Description
Hi, I would like to use cutadapt in our pipeline, which uses a database to store data and requires traceability/reconstruction of the various steps, storing cutoff points for the adapter clipping along with the original sequences. To do that it would be practical to have an option to also produce a tab separated file holding the read identifier and the four cutoff offsets (two for the forward and two for the reverse reads in pairs where the adapter is found). Offsets for the right end should be given from the end of the sequence (i.e. number of bases cutted from the right end as opposed to the offset from the beginning of the read).
Would that be feasible? Where should I look in the source tree to implement such a feature?
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Research direction
No source files, tests, or entry points are named in the issue. Start by tracing paired-read adapter trimming and output generation, then define the tab-separated record format and verify that forward and reverse cut offsets can be reconstructed for reads where adapters are found.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 30/100