I have spent several hours trying to figure out the best approach to do this. It would have been quicker to manually do it, but I will need to do this in future.
I have 40 paired-end RNAseq samples that were read across 5 lanes. I therefore have 400 fastq.gz files that I would like to process in Kallisto. The file name structure is as follows:
'string' is the same for every file
I want to concatenate the 5 lane files for each of the 40 samples, rather than running Kallisto for 200 paired end samples (is this the correct approach?).
Can someone please advise on the best way to concatenate these files? I have some knowledge of python and could do a bash script if someone could explain what each part means. Thank you