Which gene annotation file in UCSC is equivalent to the gene annotation file that is NOT 'abinitio' or 'chromossome' in ensembl?

Question

[salamandra]

In ensembl it's easy to identify the anotation table with the genes for a genome: (we select the .gtf file that is NOT ‘abinitio’ or chromossome). But as I have a ucsc genome version, I heard should use the corresponding UCSC gene anotation file.

However, there are many options of annotation files in UCSC. This page has all of them.

Which one should I use?

I just want regular gene anotation, the equivalent to ensembl gene file that is NOT abinitio or chromossome.

[salamandra]

Tried the table browser and it seems for recent assemblies, e.g. human GRCh38/hg38, there's only 'Old UCSC genes'. Then I found this page that says the default is now to use GENCODE for GRCh38 asembly. So better to use the GENCODE as is updated.

[GenoMax]

Be careful about jumping around with sequence/annotations. GENCODE provides official annotation for human and mouse genomes. Other providers may add their own (Ensembl/HAVANA, NCBI and UCSC) on top. While the underlying sequence should be identical (for a particular genome build) you would still want to use sequence/annotation combination from a single provider since mixing/matching can cause problems downstream (with read counting/visualization etc). This mainly happens since providers use different naming schemes for chromosomes.

[salamandra]

Ok. And, should I use the 'Old UCSC genes' with human GRCh38/hg38 assembly or use the with the older hg19 version, or it doesn't matter?

Answer 1

[GenoMax]

You can export a GTF file using table browser. It is not on the page you linked as I recall.