Hi guys, I have a total of 32 samples from RNAseq, paired end (Illumina). For each sample I have 4 different fastq files for 4 different lanes (and forward and reverse). So in total I have 4 forwards and 4 reverse fastq files for each sample. I was wondering if it could be possible and recommendable to merge the 4 fastq files for each forward and reverse and do the QC analysis with fastqc. Or is better to trimming each fastq file independently and then merge?
Many thanks in advance!