I received my paired end sequences with 4 files per sample, 2 files per read. I want to concatenate the two files of each read and only have R1 and R2 for each sample.
Manually it works:
cat /media/Ea2/Ea2_FKDL220291524-1A_H22M7DSX5_L2_1.fq.gz /media/Ea2/Ea2_FKDL220291524-1A_HYVFNDSX3_L3_1.fq.gz > /media/Ea1/Ea1_concatenated_R1.fq.gz
but I want to do it for multiple sequence files:
Ea1
Ea2
Ea3
etc...
I tried doing it for multiple files for the R1 files first:
cat /media/Ea*/Ea*_*-1A_*_L*_1.fq.gz /media/Ea*/Ea*_*-1A_*_L*_1.fq.gz > /media/Ea*/Ea*_concatenated_R1.fq.gz
it did not work.
I tried giving the command a list with the names of each samples like this:
for i in $(cat /media/list_for_con.txt) do cat /media/$i/$i_*-1A_*_L*_1.fq.gz /media//$i/$i_*-1A_*_L*_1.fq.gz > /media/$i/$i_concatenated_R1.fq.gz
It did not work. Even if it would work it would allot me to adress the R1 and then change it and do the R2 files.