From 08170f9f97cb8f0c6a0109e606e7ae77ec59f42b Mon Sep 17 00:00:00 2001
From: srikeerthanakuchi <108755938+srikeerthanakuchi@users.noreply.github.com>
Date: Fri, 28 Jun 2024 11:40:09 +0100
Subject: [PATCH] Update GeneOntologyPathway.md

---
 docs/GeneOntologyPathway.md | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/docs/GeneOntologyPathway.md b/docs/GeneOntologyPathway.md
index b2bf150..81e1ae5 100644
--- a/docs/GeneOntologyPathway.md
+++ b/docs/GeneOntologyPathway.md
@@ -341,5 +341,20 @@ dev.off()
 
 ```
 
+1. Create a new directory “RNA-seq” in your home directory.
+2. In the “RNA-seq” directory, generate a soft link to the following files:
+
+```bash
+	fastq files - /home4/VBG_data/SUBSAMPLED
+	genome - /home4/VBG_data/RNASeq/Human.fa
+	GTF - /home4/VBG_data/RNASeq/Homo_sapiens.GRCh38.107.gtf
+```
+
+3. Perform QC, adapter-trimming, read mapping and generate bam files
+Generate count data from bam files 
+4. Perform DE analysis using edgeR (check whether the order of the samples match the edgeR script, header is absent)
+5. Perform GO (ORA and GSEA) and pathway analysis (MSigDb GSEA)
+
+