Dashes or N's in remap consensus
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- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
Currently, we use N's in the remap consensus sequence for bases at the start of the seed that did not map any reads. We use dashes when all the reads contain a deletion relative to the seed, and that deletion is not a multiple of three.
Look at the bowtie2 documentation, or run some experiments to see if the remap results will be any different when switching to dashes or N's.
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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
Start by reading the Bowtie2 documentation on consensus handling, then run remap experiments using dashes and N's for the described deletion and unmapped-seed cases. Compare the resulting remap outputs; done means determining whether either representation changes the results and documenting the evidence and recommended behavior.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100