RNA-seq reads to counts with pair-end data

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.

Hi @omer_p,
currently FASTQC doesn’t accept pared-end reads as input; you can combine the trimmed reads pair 1 and trimmed reads pair 2 files in a single file (for example by using concatenate datasets and the use it as input for FASTQC.


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