Create a full command line executable workflow for RNA-Seq on PBMC Samples.

KastanDay / ML4Bio

LLMs to execute Bioinformatics workflows, esp. RNA-seq

MIT License

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Create a full command line executable workflow for RNA-Seq on PBMC Samples. #3

Open KastanDay opened 1 year ago

KastanDay commented 1 year ago

Experiment Type: RNA-Seq Sequencing of total cellular RNA

Workflow Management: Bash/SLURM Scripting and job scheduling

Software Stack: FastQC MultiQC STAR RSEM samtools DESeq2

What else to know about the pipeline? I am working PBMC samples collected from patients that are undergoing immunotherapy.

You should write a series of bash scripts and R scripts that can accomplish this task. Open a PR with those scripts when you're done.

lil-jr-dev[bot] commented 1 year ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.