LewisLabUCSD / LewisLabUCSD/Mito_Trace
From bam to UMIs and cell filter
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- Dominant language
- Jupyter Notebook
- Stars
- 0
- Forks
- 0
- PR merge metrics
- No merged PRs in 30d
Description
Can we use the cellranger toolkit to get the cells to filter out?
Need to use bam2fastq since our downloaded fastq is not complete.
Contributor guide
No contributing guide indexed for this repository
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 files, tests, or entry points are named. Start by determining how the repository currently handles downloaded FASTQ and BAM inputs, then review the intended cellranger and bam2fastq workflow. Done should mean a documented, reproducible way to recover cells for filtering and obtain complete FASTQ data.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100