Reads with / characters in the read names cause the pipeline to fail
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Description
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Description of the bug
If / characters are in the read names, then the pipeline will fail at the dedup step. This is caused, however, by STAR truncating read names based on the / character. This removes the UMI information which was added earlier in the pipeline, causing the dedup step to fail.
Steps to reproduce
Steps to reproduce the behaviour:
Running the pipeline with reads with a / in the read name. Example
Expected behaviour
Either a verbose error message saying that the reads are incompatible, or automatic removal or replacement of the / characters.
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
Start by reproducing the failure with the ENA example linked in the issue, then inspect the STAR mapping step and the subsequent dedup step to confirm where read names are truncated. Done means the pipeline either handles read names containing / characters or reports a clear incompatibility error before deduplication.
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Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100