I tried to obtain the differential expression genes using cuffdiff (version 1, and version 2) , detailed command as follow,

cuffdiff -q -p 20 -o . -L s1,s2 ./hg19_annotation/gencode.v12.annotation.gtf s1/accepted_hits.bam s2/accepted_hits.bam

when command finished, in the gene_exp.diff, there are 53910 genes; but in the gtf (gencode.v12.annotation.gtf ) there are 53934 genes. then I compare gene id in gene_exp.diff and gencode.v12.annotation.gtf, the 24 missed genes are

'ENSG00000207744.1', 'ENSG00000206794.1', 'ENSG00000262228.1', 'ENSG00000252006.1', 'ENSG00000253739.1', 'ENSG00000235284.1', 'ENSG00000207103.1', 'ENSG00000200319.1', 'ENSG00000257772.1', 'ENSG00000231587.1', 'ENSG00000262839.1', 'ENSG00000259197.1', 'ENSG00000238752.1', 'ENSG00000254474.1', 'ENSG00000249020.1', 'ENSG00000243108.1', 'ENSG00000207792.1', 'ENSG00000258335.1', 'ENSG00000255137.1', 'ENSG00000226572.1', 'ENSG00000207727.1', 'ENSG00000256239.1', 'ENSG00000206673.1', 'ENSG00000253296.1'

I do not know why these genes are not shown?