From f5a79a70fd41995fb944706c1ad7fe342f6245fb Mon Sep 17 00:00:00 2001
From: Ayushi Agrawal
 <88406934+ayushi-agrawal-gladstone@users.noreply.github.com>
Date: Wed, 13 Jul 2022 16:07:41 -0700
Subject: [PATCH] Delete all_steps.sh

---
 intro-rna-seq/all_steps.sh | 37 -------------------------------------
 1 file changed, 37 deletions(-)
 delete mode 100644 intro-rna-seq/all_steps.sh

diff --git a/intro-rna-seq/all_steps.sh b/intro-rna-seq/all_steps.sh
deleted file mode 100644
index 20bd5a2..0000000
--- a/intro-rna-seq/all_steps.sh
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/bin/bash
-
-#This script should be run on the dev3 node of the UCSF Wynton HPC cluster
-#before running this script, do the following
-##  1. transfer the workshop files from your local computer to your wynton account
-##     {local}$ scp -r Downloads/Intro_to_RNA-seq_data_analysis/ alice@dt2.wynton.ucsf.edu:~
-##  2. create the singularity container rna_seq_container.sif on wynton using the below command
-##     [alice@log1 ~]$ singularity build rna_seq_container.sif docker://nfcore/rnaseq 
-
-cd ~/Intro_to_RNA-seq_data_analysis/
-
-singularity exec rna_seq_container.sif fastqc Bacteria_GATTACA_L001_R1_001.fastq
-
-singularity exec rna_seq_container.sif cutadapt \
--a file:Adapter_Sequence.fasta \
--o trimmed.fastq \
-Bacteria_GATTACA_L001_R1_001.fastq
-
-singularity exec rna_seq_container.sif fastqc trimmed.fastq
-
-singularity exec rna_seq_container.sif mkdir star_index
-
-singularity exec rna_seq_container.sif STAR \
---runMode genomeGenerate \
---genomeDir ./star_index \
---genomeFastaFiles rDNA_sequence.fasta \
---genomeSAindexNbases 3
-
-singularity exec rna_seq_container.sif STAR \
---genomeDir ./star_index \
---readFilesIn ./trimmed.fastq
-
-singularity exec rna_seq_container.sif featureCounts \
--a rDNA.gtf \
--t CDS \
--o counts.txt \
-Aligned.out.sam