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Remove whitespace
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donald committed Sep 13, 2022
1 parent 3ad1bcb commit 303e16d
Showing 1 changed file with 6 additions and 6 deletions.
12 changes: 6 additions & 6 deletions Adapting_new_script_for_computing_cluster.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -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

Expand All @@ -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

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