20 months ago
Make a bash script with your trimmomatic command:
java -jar trimmomatic-0.35.jar SE -phred33 $1 "`basename $1 .fastq.gz`.trimmomatic_out.fastq.gz" ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
$1 is your input file, and
basename will remove the
.fastq.gz and replace with the suffix
.trimmomatic_out.fastq.gz. Save as
List all of your single end files in a a file as a list (single column):
SE_files.txt. If they are all in one dir:
ls -1 *.fastq.gz > SE_files.txt. Then pass each of your single end files to the trimmomatic command.
cat SE_files.txt | xargs -n 1 bash run_all_trim.sh
If you have a lot of files, and don't want it to hangup, and to run in the background:
cat SE_files.txt | xargs -n 1 nohup bash run_all_trim.sh &
top to check periodically that it's still running.