Hi Nikelle,
the DESeq2 input is - as far as I understand - is a two-column file with first column being gene ID, and the second column - the number of reads per gene.
To make such a file from the STAR's ReadsPerGene.out.tab file, you would need to
1. Use the first column of ReadsPerGene.out.tab as the first column of the input to DEseq2
2. Use the 2nd, 3rd or 4th column of ReadsPerGene.out.tab as the 2nd column depending on the strandedness of your library:
2nd column - for unstranded data
3rd column - for 1st read agreeing with RNA strand
4th column - for 2nd read agreeing with RNA strand (typical for Illumina stranded Tru-seq)
3. Cut out the first 4 lines of the ReadsPerGene.out.tab that contain counts for non-genic read (unmapped/multimappers/ambiguous/noFeature).
For instance for Illumina stranded Tru-seq you would use
$ awk 'NR>4 {print $1 "\t" $4}' ReadsPerGene.out.tab DEseq.input
Cheers
Alex