I wanted to ask whether the order of genes in two different BAM files when running cuffdiff is important or not? To be more precise:
I have two BAM files which are the result of applying tophat over two samples from different experiments but the same reference genome (hg19).
Do you think that since they are from different experiments and the order of related genes may vary in these BAM files, I can obtain a meaningful cuffdiff result from them or not? Thank you in advance