I have used `featureCounts` to get the read counts one a gene level with the following command:

    featureCounts -a gencode.gtf -F GTF -p -s 2 -T 8 -o sample.txt sample.sorted.bam

I'm interested in extracting the counts on a transcript level. My data is paired end and reverse stranded. I'm a bit confused with command I have to use to get the counts on transcript level [featureCounts manual][1]

Can anyone please tell me how to get the counts on transcript level? thanq

  [1]: http://bioinf.wehi.edu.au/featureCounts/
You'll probably want to use `RSEM` or `stringTie`