svpipaliya / bulk-rnaseq

This repo contains scripts and workflows for performing bulk transcriptomics analyses

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Bulk Transcriptomic Analyses for Human RNA-Seq Data

This repo contains bash scripts and a snakemake workflow for performing bulk transcriptomic analyses, specifically using samples originating from human tissue/cell culture. Workflow can be used for sequencing reads in paired or single-end form generated using Illumina HiSeq/MiSeq or BGI Genomics.

  • Briefly, the steps consist of quality control to assess read contamination and base quality, adapter detection and trimming (Illumina only; please provide adapter sequences in-case using another technology), read alignment against the human reference genome/transcriptome (build hg38/GRCh38), quality control of the aligned BAM files, sorting and indexing of BAM files, gene-level quantification, differential gene expression analyses, gene set enrichment analyses, and protein pathway analyses.

Tools and dependencies:

The Snakemake workflow is still under progress and contents will be modified frequently. Below is the current DAG of the rules used in the workflow.

Screenshot 2023-01-23 at 17 31 11

An additional README is available on how to specifically run the snakemake workflow in a slurm HPC environment. Instructions on workflow installation and setup using Conda/Mamba are also detailed.

Author: Shweta Pipaliya

Date Updated: 17.2.2023

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This repo contains scripts and workflows for performing bulk transcriptomics analyses


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