Importing RNA-seq Gene Count Data from GEO
For RNA-seq series registered in GEO, text files containing gene counts are often provided in the Supplementary Files. Even if these are absent, text files with gene counts calculated by GEO are frequently available. (https://www.ncbi.nlm.nih.gov/geo/download/?acc=[GSE accession number])
While using Supplementary Files avoids discrepancies with the paper, differences in FASTQ file processing among authors make them unsuitable for integrating data from different series. If you anticipate collecting multiple datasets for reanalysis, we recommend using Gene Counts calculated by the GEO's standardized protocol.
In any case, if you can obtain the Gene Count table, you can easily start reanalysis without needing to process FASTQ files yourself. This video demonstrates how to import such a GEO Gene Count text file into the Subio Platform in both supplementary and GEO-calculated versions.
Please also see this topic for collecting experiment parameters.