Hi everyone, I am trying to merge three distinct dataseries on GEO (all with same cell types) to perform a meta-analysis. is there a way to do this using galaxyproject? cause I tried to but the first problem is that I dont know a convenient way to upload my data into my history: these dataseries I am working with are pretty large in sample number (one of them has 800 samples) and by using "get data" (then EBI SRA) I have to find and input all samples' accession number one by one, which is so time-consuming (considering each sample has two fastq files). I would be so grateful if someone helps me with this and of course, to introduce articles about how to do these types of meta analysis cause I am a wet lab biologist and completely new to bioinformatics :) thanks!
You would want to use sra-toolkit to download the files. Regarding the meta-analysis, it's not straight-forward at all since library prep, sequencing etc. was all done differently so you might end up with differences that stem from experimental procedure rather than actual biology.