I have some RNA-seq fastq files which I aligned to GRCh38 with STAR. The RNA-seq protocol was stranded. I used --quantMode GeneCounts option in STAR. An example of one of the count files can be seen below. I'm looking to run DESeq2 and wanted to check if the right method is to use the counts from the third column?
Ah okay, so the column with lower count values is defined as the reverse strand?
No. Read the documentation.