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@IdoBar
Forked from danielecook/FastQC_aggregate.sh
Created July 16, 2017 23:12
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Examine Fastqc reports in aggregate; brings images, statistics, and summaries together. #fastq
# Run this script in a directory containing zip files from fastqc. It aggregates images of each type in individual folders
# So looking across data is quick.
zips=`ls *.zip`
for i in $zips; do
unzip -o $i &>/dev/null;
done
fastq_folders=${zips/.zip/}
rm -rf fq_aggregated # Remove aggregate folder if present
mkdir fq_aggregated
# Rename Files within each using folder name.
for folder in $fastq_folders; do
folder=${folder%.*}
img_files=`ls ${folder}/Images/*png`;
for img in $img_files; do
img_name=$(basename "$img");
img_name=${img_name%.*}
new_name=${folder};
mkdir -p fq_aggregated/${img_name};
mv $img fq_aggregated/${img_name}/${folder/_fastqc/}.png;
done;
done;
# Concatenate Summaries
for folder in $fastq_folders; do
folder=${folder%.*}
cat ${folder}/summary.txt >> fq_aggregated/summary.txt
done;
# Concatenate Statistics
for folder in $fastq_folders; do
folder=${folder%.*}
head -n 10 ${folder}/fastqc_data.txt | tail -n 7 | awk -v f=${folder/_fastqc/} '{ print $0 "\t" f }' >> fq_aggregated/statistics.txt
rm -rf ${folder}
done
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