Adapter matches in the middle of a read masked with N
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- Dominant language
- Python
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Description
By default, the cutadapt removes the rest (after the adapter) of the sequences. If my sequences like:
ADAPTERmysequenceoneADAPTERmysequencetwoADAPTER
I will get mysequenceone in the output file by default.
When using -r, I will get mysequencetwo in the output.
However, I want to simultaneously keep mysequenceone and mysequencetwo in the output file, so I thought I could use --action mask to task the ADAPTERs with N first, then split this read into two pieces. However, the output looks like the following:
NNNNNNNmysequenceoneNNNNNNNNNNNNNNNNNNNNNNNNNNN
In the future version of cutadapt. Can it label the adapter sequence alone?
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 issue’s example with the current --action mask behavior and inspect how adapter matches in the middle of a read are handled. The desired behavior is to retain both non-adapter segments while masking or otherwise labeling the adapter sequences, but the issue does not name files or tests, so the implementation scope needs clarification.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 30/100