Hey all, I had a doubt regarding the output generated by featureCounts. So, what would be the difference in output between the following commands:
featureCounts -p -s 2 -F GTF -t exon -a annotation.gtf -o counts.txt sample.bam featureCounts -p -s 2 -F GTF -t gene -a annotation.gtf -o counts.txt sample.bam
From what I understand, the second command will only read the lines in the GTF which have 'gene' in the 3rd column while the first command will count the exon lines. Also, the sum of the reads for all exons of a gene should be the same as the number of reads for the gene as a whole. So, should the output file have the same counts for both?