From 63324d0ab297842bc686bda68135adbe5b9b5aea Mon Sep 17 00:00:00 2001
From: Matteo Barcella <barcella.matteo@hsr.it>
Date: Tue, 18 Feb 2025 17:03:47 +0000
Subject: [PATCH] Update README.md

---
 bulkRNAseq/README.md | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/bulkRNAseq/README.md b/bulkRNAseq/README.md
index 139597f..e2bc73f 100644
--- a/bulkRNAseq/README.md
+++ b/bulkRNAseq/README.md
@@ -1,2 +1,30 @@
+**Bulk RNAseq** data analysis workflow includes the following steps:
 
-
+1. Quality control by [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+2. Trimming of bad quality reads with [TrimGalore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
+3. Alignment with [STAR](https://github.com/alexdobin/STAR)
+    <details><summary>Running command</summary>
+            "STAR " +
+            "--runThreadN {threads} " +
+            "--genomeDir {input.genome} " +
+            "--readFilesIn {params.trim_seq} " +
+            "--outSAMstrandField intronMotif " +
+            "--outFileNamePrefix {params.aln_seq_prefix} " +
+            "--outSAMtype BAM SortedByCoordinate " +
+            "--outSAMmultNmax 1 " +
+            "--outFilterMismatchNmax 10 " +
+            "--outReadsUnmapped Fastx " +
+            "--readFilesCommand zcat "
+    </details>
+4. Gene expression quantification with [FeatureCounts](https://academic.oup.com/bioinformatics/article/30/7/923/232889)
+    <details><summary>Running command</summary>
+            "featureCounts " +
+            "-a {input.annot} " +
+            "-o {output.fcount} " +
+            "-g gene_name " +
+            "-p -B -C " +
+            "-s {params.strand} " +
+            "--minOverlap 10 " +
+            "-T {threads} " +
+            "{input.bams} "
+    </details>
-- 
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