I have a folder of a plate run from an illumina machine, which in it has many folders of different samples each with four files from illumina. I want to combine the two left R1 files to one gz file and combine the two right R2 files to one file for each sample (folder). I can't see an automated version rather than just gzip each subfolder in turn but likely there is a bash way which completely missing?
i.e. within folder "plateK"
Sample1_folder
sampAR1_a.gz, SampAR1_b.gz, SampAR2_a.gz, SampAR2_b.gz
Sample2_folder
sampBR1_a.gz, sampBR1_b.gz, sampBR2_a.gz, sampBR2_b.gz
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written
by
rob234king
2 answers
If you want to concatenate all files in each depth=1 subdirectory you could do something like:
for i in `ls -d */`; do
cat ${i}*R1*.gz > ${i}R1.gz
cat ${i}*R2*.gz > ${i}R2.gz
done
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written
by
Keith Callenberg
You can cat gzip files to concatenate them.
cat sampAR1_a.gz sampAR1_b.gz > sampAR_1.fq.gz
cat sampAR2_a.gz sampAR2_b.gz > sampAR_2.fq.gz
Be very careful to maintain correct order in the final files otherwise you will have a lot of discordant read pairs.
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written
by
mark.ziemann
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I think that's not really a bioinformatics question, however you can use
tarwith--includeoption,tar -c -f R1.tar --include='*R1_*.gz'or similar should work, seeman tar.