I’m new to galaxy and working on an RNAseq experiment where I have 2 conditions with 3 replicates for each one. The NCBI SRA accession number is SRP154796.
To perform DGE analysis on DESeq2 or edgeR, I need to have a separate count file for each replicate (that is what I understood after reading a few posts here). However, I don’t have access to the original fastq files on NCBI and can only download a single SRA file where all the replicates are merged.
I’ve used a tool on galaxy to convert my SRA file to fastq format but I obtain a single fastq file with interleaved reads. When I download the files from ENA, the reads are separated in forward/reverse but the replicates are still merged :
I couldn’t find a way to separate the replicates, hence I only have 2 count files for DESeq/edgeR and constantly get an error.
Does anyone know how I can get the original fastq files for all the replicates? Or if the problem comes from the way I’m using DESeq2/edgeR?
Thank you in advance.