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