Added a bash script with all steps and updated slide deck

intro-rna-seq/all_steps.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+fastqc Bacteria_GATTACA_L001_R1_001.fastq
+
+cutadapt \
+-a file:Adapter_Sequence.fasta \
+-o trimmed.fastq \
+Bacteria_GATTACA_L001_R1_001.fastq
+
+fastqc trimmed.fastq
+
+mkdir star_index
+
+STAR \
+--runMode genomeGenerate \
+--genomeDir ./star_index \
+--genomeFastaFiles rDNA_sequence.fasta \
+--genomeSAindexNbases 3
+
+STAR \
+--genomeDir ./star_index \
+--readFilesIn ./trimmed.fastq
+
+featureCounts \
+-a rDNA.gtf \
+-t CDS \
+-o counts.txt \
+Aligned.out.sam