What are people using to search for raw fastq files in GEO or SRA made available from past publications for a specific cell? I am currently using SRA search database with key words, specifying in the search term:
GM12878[All Fields] AND cluster_public[prop]
However this misses some downloadable data.
There is a nice post here (How to download raw sequence data from GEO/SRA) to retrieve these files using fastq-dump, but this assumes the GEO accession number, or the SRA project page, is already known.
Is there another searchable engine that helps to search for these more efficiently that people are currently using? I see there is an R package called GEOquery to help with GEO searches - I haven't looked at it yet but if it is possible to limit by only certain files and cell types, this may be the best option.