I have analyzed RNA-seq data by mapping with RNA STAR and then performing featureCounts, followed by DESeq2 and other downstream analyses. Initially, I conducted the analysis at the gene level. However, my colleagues have now decided that they want to see the analysis at the exon level.
I adjusted the featureCounts settings by enabling the “on feature level” option. However, when I use gene_id as an identifier, I get repeated occurrences of the gene name corresponding to the number of exons, for example:
Gene A 0
Gene A 0
Gene A 1
When I use exon_id as an identifier, the results are even less useful. Unfortunately, I cannot use both the gene and exon IDs simultaneously in the “GFF Gene Identifier” field, as this results in an error.
How can I resolve this issue so that I obtain counts with both the gene ID and exon number?
I wonder if DEXseq instead of DESeq2 is what you want?
Search the tool panel at the UseGalaxy.eu server to find it. Notice there are two modes with the upstream tool: one is a special way to generate a GTF with DEXSeq-Count that has all of the exon-level information encoded in a way these tools can understand. Run that first. Then use that GTF to actually generate the counts in the other mode. Then the main tool can generate the DE.