I am learning how to analyse NGS data. I have a data for 192 samples. These were obtained through a targeted sequencing library prep.
I have 192 samples, but technically I have received 2 files for each sample. For example:
Presumably the reason there are 2 files is because paired-end sequencing was performed. I've been reading around on the various steps of NGS analysis but I can't seem to find an answer to the following question:
How to handle paired-end reads? Do you do have to merge them and if so when? Before alignment presumably? Also, do I have to uncompress the fastq.gz before I do anything? I am very new to NGS so apologies if these are really basic questions. Thanks.