Move insertions to expected locations
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- Dominant language
- Python
- Stars
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- Avg merge
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Description
If there are substitutions near an insertion, bowtie2 can get confused about where exactly to put the insertion. Use the same technique as Recall to move the insertions to expected locations. Here's Conan's description:
For PR/RT (in recall we do them together), they are at amino acid position 35, 41, 99, 168 (69 of the RT). Most of the time it's just 35 of the protease or 69 in the RT.
For Integrase, there is one insertion at 288, which is a bit weird because it happens right before the stop codon. It doesn't cause any resistance (that we know of), and it's pretty random in size.
I shift them up to 13 nucleotides in either direction.
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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 locating Recall's existing insertion-shifting technique and the Bowtie2 handling described in the issue. Determine how insertions near substitutions are represented, then verify that they are shifted by up to 13 nucleotides to the expected positions for PR/RT and Integrase without changing other results.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 28/100