I have two groups of patients; for each patient I have an output file (RNA-seq) contains this information
readcounts_union readcounts_intersectionNotEmpt genelength R/FPKM_union R/FPKM_intersectionNotEmpt ENSG00000000003.10 8 8 3688 1.06120392730222 1.05722142116966 ENSG00000000419.8 31 31 4032 3.76132572546529 3.74721015127372
reads that overlap a single feature are included in the count for that feature; reads that overlap more than one feature are not included in the counts
regions that are shared between features are excluded; reads that overlap a remaining region are included in the count for the feature that includes that region; reads that overlap regions from more than one feature are not included in the counts
readcounts_union normalised for gene length and sequencing depth
readcounts_intersectionNotEmpty normalised for gene length and sequencing depth
I want to do differential expression analysis between groups but I don't know which column I should use for DESeq2
Anybody familiar with such a format?