I have 400 fastq files from different samples in two sequencing runs. Both runs were on Illumina Hiseq. How i can merge the .fastq files of both runs for each sample, and in one step..For sure we have to keep R1 and R2 separate ..I know that we can just merge the .fastq files of both runs using cat..but i have to use this only for one sample…and than i have to repeat this many times for all the samples..and i have more than 100 samples... What command do i use ?? any folder to prepare?
Thank you for helping me