Delete all_steps.sh

intro-rna-seq/all_steps.sh

@@ -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