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intro-rna-seq/all_steps_wynton.sh

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+#!/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