combining multiple gz files in subfolders
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0
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9.2 years ago
rob234king ▴ 610

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
bash • 5.2k views
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I think that's not really a bioinformatics question, however you can use tar with --include option,

tar -c -f R1.tar --include='*R1_*.gz' or similar should work, see man tar.

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5
Entering edit mode
9.2 years ago

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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4
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9.2 years ago
mark.ziemann ★ 1.9k

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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0
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Question sir, If i had 300 pairs to file to combine, please help with the appropriate script.

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