Merge ATAC-seq multiple lanes
#! /bin/bash
# unzip all the gz files in a folder
ls | grep '.gz' | while read line; do gzip -d $line; done
# merge fastq sequence lanes
echo "merging ... ATAC-seq_R1"
cat ATAC-seq_L001_R1_001.fastq ATAC-seq_L002_R1_001.fastq ATAC-seq_L003_R1_003.fastq ATAC-seq_L004_R1_001.fastq > ATAC-seq_R1.fastq
echo " Done! "
echo "merging ... ATAC-seq_R2"
cat ATAC-seq_L001_R2_001.fastq ATAC-seq_L002_R2_001.fastq ATAC-seq_L003_R2_001.fastq ATAC-seq_L004_R2_001.fastq > ATAC-seq_R2.fastq
echo " Done! "
# gzip fastq files
ls | grep '.fastq' | while read line; do echo "$line is compressing..."; gzip $line; echo "Done!"; done
calculating time
#! /bin/bash
start_time=$(date +%s)
echo "Starting Time : $(date +%Y)/$(date +%m)/$(date +%d) - $(date +%H)h/$(date +%M)m/$(date +%S)s"
# unzip all the gz files in a folder
ls | grep '.gz' | while read line; do gzip -d $line; done
echo "Ending Time : $(date +%Y)/$(date +%m)/$(date +%d) - $(date +%H)h/$(date +%M)m/$(date +%S)s"
end_time=$(date +%s)
# To get execution time
dt=$(echo "$end_time - $start_time" | bc)
dm=$(echo "$dt/60" | bc)
ds=$(echo "$dt-60*$dm" | bc)
printf "Total runtime : %d m %d s", $dm, $ds
md5sum
cat sequence_R1_002.fastq.gz | md5sum > out.txt
# for loop
for file in *fastq.gz; do md5sum "$file" > "${file//.fastq.gz}".md5; done
# for loop(wrong code)
for file in *fastq.gz; do md5sum "$file" > "file".md5; done
change disk (Cygwin64)
cd f:/
chmod, tar
# run script
chmod +x *.pl
./*.pl
tar -xvf *.tar
tar -t *.tar
csplit -s -z *.fa '/>' '{*}'