Hi,

Assuming that you're running featureCounts inside R, a similar question was already answered:

Output from featureCounts() as input to DESeq2

I used previously featureCounts command-line tool, but not inside R. The output of the command-line tool is a text file per sample or one for all the samples, depending on how you run the tool, with several columns (with gene id, read-length, genomic coordinates, counts, etc).

From your description above, I'm assuming that the output of featureCounts R function is a rds file (read more about rds files in R). If so, you can import this rds file into R by doing the following:

counts <- readRDS("path_to/rds_file/file.rds")

Where "path_to/rds_file/file.rds" is a string to the output .RDS file that you have. This will import this object back to R. Although I'm not familiar with the data structure of this and you may need to parse this data in order to provide it to DESeq2.

Perhaps looking into the previous link on Biostars that answers to a similar question is the best way to go.

I hope this helps,

António