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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. Open a new pull request (on a separate branch) and comment the PR number here when you're done #45

Open rohan-uiuc opened 10 months ago

rohan-uiuc commented 10 months 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.

Use the data files existing in Report_WholeBrain as input for this workflow.

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.