diff --git a/intro-rna-seq/Intro_to_RNA-seq_concepts.pptx b/intro-rna-seq/Intro_to_RNA-seq_concepts.pptx index ec6e886..f53b86d 100644 Binary files a/intro-rna-seq/Intro_to_RNA-seq_concepts.pptx and b/intro-rna-seq/Intro_to_RNA-seq_concepts.pptx differ diff --git a/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip b/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip index 478ca1b..5f7ffb0 100644 Binary files a/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip and b/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip differ diff --git a/intro-rna-seq/all_steps.sh b/intro-rna-seq/all_steps.sh new file mode 100644 index 0000000..d404af0 --- /dev/null +++ b/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