combining multiple gz files in subfolders

Question

[rob234king]

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

[Michael]

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.

Answer 1

[Keith Callenberg]

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

Answer 2

[mark.ziemann]

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.

[alnus]

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