Hello,
With regards to recount3: I was wondering about SRA samples associated with multiple FASTQ files (ie. multiple runs). From looking it seems like these were not merged prior to the rail pipeline run, as results are at the level of SRR IDs. Therefore it seems like when you want to do a search/analysis you always need to run a function to aggregate counts/coverage/whatever for SRR ids that actually represent a part of a sample, not the whole sample. What's the most efficient way to do this - I have the samples.tsv, so presumably I need to aggregate results that share the same sample_acc? very sorry if I've missed documentation about this! Is there some functionality in one of the packages for this? Or how do people go about doing this?
eg. this sample has 8 runs, which have been run through the analysis pipeline separately: https://www.ncbi.nlm.nih.gov/sra?term=SRX5027105&cmd=DetailsSearch
I am particularly looking at the general QC metrics, gene counts and bigwig files.
Thanks so much for any help!
Charlotte
