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The statistics derive from the gtf file that contains only the annotation of the main chromosomes Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For details about the calculation of these statistics please see the readme_stats.txt file.
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Some of the protein coding genes are not labeled protein_coding and therein lies my problem For a detailed description of the methods and references used, see harrow et al This includes both manual and automatic annotations.
In mouse 36 were added and 49 removed.
It contains annotations on the reference chromosomes as well as assembly patches and alternative loci (haplotypes). This package loads genes from gencode gtf/gff files, groups transcripts by gene, and provides methods for transcripts, so you can find exon coordinates, cds distances and sequences. The gencode primary transcript set captures a minimal set of transcripts at protein coding genes
