I'm trying to set up a for loop to run a process on pairs of files. The names of the files look like this
36_002_CGATGT_L001_R1_005.fastq.gz 36_002_CGATGT_L001_R2_005.fastq.gz 36_002_CGATGT_L001_R1_002.fastq.gz 36_002_CGATGT_L001_R2_002.fastq.gz 62_013_AGTCAA_L001_R1_003.fastq.gz 62_013_AGTCAA_L001_R2_003.fastq.gz
I need to use each pair in the following command
sickle pe -f 36_002_CGATGT_L001_R1_005.fastq.gz \ -r 36_002_CGATGT_L001_R2_005.fastq.gz\ -o trimmed_36_002_CGATGT_L001_R1_005.fastq.gz\ -p 36_002_CGATGT_L001_R2_005trimmed_36_002_CGATGT_L001_R2_005.fastq.gz\ -s 36_002_CGATGT_L001_singles_005.fastq.gz To begin with I'm trying:
for n in *R1*; do m='basename $n R2' ; echo $m; done but clearly this approach isn't working because the both the front and back of the file name are important. Do I need to rename files so the R1 and R2 are the last part of the name? Which would be awkward but not impossible
