Coordinate system BadRead
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 302
- Forks
- 25
- PR merge metrics
- No merged PRs in 30d
Description
Describe the bug
BadRead reports in the header the coordinate of the read relative to the original genome.
@3d39fc0e-4092-3f08-05b3-1a216974b035 NC_000913.3,-strand,1264589-1277307 length=12713 error-free_length=12718 read_identity=99.898%
Often this coordinate is correct. However, when mapping all reads back to the reference genome, it becomes clear that the coordinates are often wrong.
When aligning the read with minimap, the true coordinates on the genome is: 3371966
3d39fc0e-4092-3f08-05b3-1a216974b035 16 NC_000913.3 3371966 60 6370M1I487M1D1772M1D1329M1I843M1D46M1D177M1D945M2D742M * 0 0
It took me 1,5 day to realize the coordinates were wrong.
Contributor guide
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
No file or test is named in the report. Start by tracing where Badread generates the BadRead header coordinate, then compare that value with the minimap alignment shown in the issue. Done means the reported coordinate matches the read's true reference-genome position, including reverse-strand reads.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100