Title about says it all. I have an eCFP sequence, the transcripts for which I would like to be able to detect in my sequencing study. I have the Mm ref genome, corresponding GTF file and separately, the full sequence for eCFP. I'm just... not sure how to to insert the sequence into my ref genome and correspondingly, note it in the GTF file. Thanks!
I'm not sure if I understand entirely. Do you know where the eCFP fragment belongs in your genome, i.e. the genomic coordinates?