I’m trying to follow the tutorial of RNA-seq reads to counts, I have pair-end data from ENA but the tutorial reffers only to single pair data. I tried to follow the training whithout buliding a collection. I trimed the reads with Trim Galore instead of Cutadapt. when I wanted to proceed with fastQC I couldn’t understand which files of my rawdata I should choose.
I’d apricceate your help with analyzing paird-end data.