diff --git a/Adapting_new_script_for_computing_cluster.sh b/Adapting_new_script_for_computing_cluster.sh index f168c5e..36ede2e 100755 --- a/Adapting_new_script_for_computing_cluster.sh +++ b/Adapting_new_script_for_computing_cluster.sh @@ -85,9 +85,9 @@ execute() { #################################### mkdir data final_bam peaks bigwig fastqc - - : Running FastQC on $id - + + : Running FastQC on $id + /project/RNAseq_Mdl_data/Konrad/FastQC/fastqc fastq/$f1 --outdir fastqc /project/RNAseq_Mdl_data/Konrad/FastQC/fastqc fastq/$f2 --outdir fastqc @@ -112,9 +112,9 @@ execute() { bedtools intersect -v -a ${id}_sorted.bam -b $blist > final_bam/${id}_sorted_blacklisted.bam samtools index final_bam/${id}_sorted_blacklisted.bam - + : Removing duplicates from ${id} using PICARD - + java -jar $PICARD MarkDuplicates INPUT=final_bam/${id}_sorted_blacklisted.bam OUTPUT=dedup/${id}_dedup.bam METRICS_FILE=dedup/${id}_dedupMetric.txt VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE samtools index dedup/${id}_dedup.bam @@ -136,7 +136,7 @@ execute() { --numberOfProcessors $THREADS \ Here I have no idea how to transfer this - + : Generating QC files for the data : Generating pearson correlation between the samples