#!/bin/bash

# concatenate two GTFs 
GTF1="/ddn/gs1/home/wardjm/Projects/Dudek/alexander_cre/chrAmigo2Cre_pBACe36_Amigo2_Transgene.gtf.gz";
GTF2="/ddn/gs1/shared/dirib/reference_genomes/mm39/mm39gencode/gencode.vM27.annotation/gencode.vM27.annotation.gtf.gz";
GTFOUT="chrAmigo2Cre.gencode.vM27.annotation.gtf.gz"

cat ${GTF1} ${GTF2} > "${GTFOUT}"