Negative mapped count in QAI
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- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
Some samples can report that they have mapped more than the number of raw reads in the QAI display, and that results in a negative count for the unmapped display. I think the problem is that some reads can be counted twice when they map to both HIV and V3LOOP.
One example is sample 2929-P26-Y02944-9F_NFLHIVDNA_S1 in the 18 Jun 2021.M05995 run.
Options to consider:
- Don't count V3LOOP at all for this display.
- Set the minimum uncounted to be 0.
- Actually go through the mapped read names and eliminate duplicates.
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First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the QAI display for sample 2929-P26-Y02944-9F_NFLHIVDNA_S1 from the 18 Jun 2021.M05995 run, then trace where HIV and V3LOOP mapped counts become the unmapped count. Compare the three proposed handling options and confirm the final display never reports a negative unmapped count.
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
- 35/100