I'm trying to concatenate a bunch of paired files into one file (for those who work with sequencing data, you'll be familiar with the paired-end read format).
For example, I have
SLG1.R1.fastq.gz
SLG1.R2.fastq.gz
SLG2.R1.fastq.gz
SLG2.R2.fastq.gz
SLG3.R1.fastq.gz
SLG3.R2.fastq.gz
etc.
I need to concatenate the two SLG1 files, the two SLG2 files, and the two SLG3 files.
So far I have this:
cd /workidr/slg/diet_manip/filtered_concatenated_reads/nonhost
for i in *1.fastq.gz
do
base=(basename $i "1.fastq.gz")
cat ${base}1.fastq.gz ${base}2.fastq.gz > /workdir/slg/diet_manip/filtered_concatenated_reads/cat/${base}.fastq.gz
done
The original files are all in the /filtered_concatenated_reads/nonhost
directory, and I want the concatenated versions to be in /filtered_concatenated_reads/cat
The above code gives this error:
-bash: /workdir/slg/diet_manip/filtered_concatenated_reads/cat/basename.fastq.gz: No such file or directory
Any ideas?
Thank you!!