Hi, Given that the genes and isoforms present in one sample are rarely identical to those present in all other samples in a given experiment, and so they need to be assembled in a consistent manner so that they can be compared, so we merge these GTF files into one single file. When merging is it advised to combine them irrespective of the treatments or group them at this stage itself into control and treatment??
Does the estimation of transcript and gene abundance be performed with respect to the merged file or with respect to the reference gene annotation file??