From 93eb12e0c9b2d5989a36d6f670668e7d1ba68946 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Mon, 25 Jan 2021 17:29:20 -0500 Subject: [PATCH] Get rid of separate script file Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- lesson1/rnaseq_analysis_on_input_file.sh | 51 ------------------------ 1 file changed, 51 deletions(-) delete mode 100755 lesson1/rnaseq_analysis_on_input_file.sh diff --git a/lesson1/rnaseq_analysis_on_input_file.sh b/lesson1/rnaseq_analysis_on_input_file.sh deleted file mode 100755 index 1996706..0000000 --- a/lesson1/rnaseq_analysis_on_input_file.sh +++ /dev/null @@ -1,51 +0,0 @@ -#!/bin/bash - -# Based on -# https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/07_automating_workflow.html -# - -# This script takes a fastq file of RNA-Seq data, runs FastQC and outputs a counts file for it. -# USAGE: sh rnaseq_analysis_on_input_file.sh - -set -e - -# initialize a variable with an intuitive name to store the name of the input fastq file -fq=$1 - -# grab base of filename for naming outputs -base=`basename $fq .subset.fq` -echo "Sample name is $base" - -# specify the number of cores to use -cores=4 - -# directory with genome reference FASTA and index files + name of the gene annotation file -genome=rnaseq/reference_data -gtf=rnaseq/reference_data/chr1-hg19_genes.gtf - -# make all of the output directories -# The -p option means mkdir will create the whole path if it -# does not exist and refrain from complaining if it does exist -mkdir -p rnaseq/results/fastqc -mkdir -p rnaseq/results/STAR -mkdir -p rnaseq/results/counts - -# set up output filenames and locations -fastqc_out=rnaseq/results/fastqc -align_out=rnaseq/results/STAR/${base}_ -counts_input_bam=rnaseq/results/STAR/${base}_Aligned.sortedByCoord.out.bam -counts=rnaseq/results/counts/${base}_featurecounts.txt - -echo "Processing file $fq" - -# Run FastQC and move output to the appropriate folder -fastqc $fq - -# Run STAR -STAR --runThreadN $cores --genomeDir $genome --readFilesIn $fq --outFileNamePrefix $align_out --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard - -# Create BAM index -samtools index $counts_input_bam - -# Count mapped reads -featureCounts -T $cores -s 2 -a $gtf -o $counts $counts_input_bam -- 2.30.2