I am trying to incorporate ERCC spike-ins into my RNA seq experiments. Everything I have read says to just append the ERCC gtf (ERCC92.gtf) onto my other gtf (GRC38.83.gtf). I tried that but am now getting an error from featuresCounts saying that my new gtf is not usable.
When I compare the ERCC92.gtf with the GRC38 format, they are totally different, so it is not surprising that simply appending doesn't work.
Has anyone been able to get these two typed of gtfs to work together?