So GRO-seq is a clever method to measure nascent RNA and I have found a nice protocol to look for active enhancers.
However, it also measures nascent mRNA transcription. So now I am wondering how to do a differential expression (DE) analysis for genes between conditions. Can I simply use standard DE analysis tools? This has been done for GRO-seq apparently (from the suppl):
The hg19 RefSeq gene list was used for all transcription level analysis. Htseq was used to get gene level read counts number from Bowtie mapped bam files. The resultant gene read count table was subjected to DESeq2 for differential gene analysis
But what confuses me is that with GRO-seq one gets mainly incomplete transcripts, right? So is the standard DE analysis still an correct approach? Would it be better to use the transcripts found by e.g., groHMM or HOMER and feed these in a DE analysis?
Input is very much appreciated! Thanks