biopipes

In Progress Personal project

R bash

Goal: Take WGS, RNAseq and ATACseq from raw reads through to one integrated multiomics readout
Inputs: Raw, demultiplexed sequencing reads from three assays
Outputs: Per-assay processed results, an integrated multiomics analysis, and the report figures
Tools: R, bash

What it does

Four modules of bash and R scripts that, run in sequence, cover the whole path from raw demultiplexed reads to integrated multiomics results and the plots that go into the report. It handles WGS, RNAseq and ATACseq, and converges the three into a single integration step.

Why it exists

It was built for a specific question: whether a treatment was having an effect on drug-resistant cancer cells. No single assay answered that on its own - the effect had to be read across genome, transcriptome and chromatin accessibility together. That meant the three pipelines could not just run side by side; they had to produce outputs that were actually integrable.

Current state

Working, but written against one dataset. The paths, references and assumptions are still specific to the experiment it was built for, and it needs generalising before it would be useful to anyone else - which is where the current free-time work on it is going. The code is not public.