Hi everyone!
After demultiplexing my samples, I have 3 .fq files per sample (total of 720 samples) containing the raw reads. I managed to merge them in a merged files using this command line
sudo cat PA001*.fq > PA001m.fq
where my .fq files per sample are PA001.fq, PA001_1.fq, PA001_2.fq etc.. and PA001m.fq is the merged file.
Now I have 720 samples in total. What would a loop look like to apply this command line to all of the samples?
Cheers!
•
written
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giulia.trauzzi •
Don't use sudo for normal functions as in sudo cat PA001*.fq > PA001m.fq. Following may work. Remove --dry-run to execute the command. Make sure that system has enough resources.
$ parallel --dry-run 'cat {=s/_2//=} {=s/_2/_1/=} {} > {=s/_2.fq//=}_m.fq' ::: *_2.fq
bash loop:
$ for i in $(ls *_2.fq); do echo "cat ${i/_2*/.fq} ${i/_2/_1} $i > ${i/_2/_m}";done
Remove echo after checking the dry-run.
without bash loop:
$ find * -type f -name '*.fq' ! -name '*_*.fq' -exec bash -c 'cat {} ${0/./_1.} ${0/./_2.} > ${0/./_m.}' {} \;
Please take a backup of files before you proceed or try with example files in a test directory.
You could simplify it a bit with
parallel --dry-run 'cat {=s/_.*(?=\.fq$)/*/=} > {=s/_2.fq/_m\.fastq/=}' ::: *_2.fq
I modified the code to avoid that problem.
Hi, thanks for your help.
As I am a real beginner here, I struggle to understand the logic of the code. Also for each of my samples I have 3 or 4 files or 5 it changes throughout the batch, would the code still apply? I am running it on a copy of my samples.
Thanks
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dangerous.