Difference between Basic and Comprehensive Gencode Genes track

[Santagostino Marco]

Dear Sir/Madam,

what is the difference between Basic and Comprehensive Gencode Genes tracks? According to the track information page, the basic track is a subset of the comprehensive one, what is missing?

Regards,

Marco Santagostino

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Marco Santagostino, PhD
Laboratorio di Biologia Molecolare e Cellulare
Dipartimento di Biologia e Biotecnologie, University of Pavia
Via Ferrata, 9 - 27100 Pavia, Italy

Post Box: Via Ferrata, 1 - 27100 Pavia, Italy
Tel.:     +39 0382 985540
Fax:     +39 0382 528496
e-mail: marco.san...@unipv.it

[Matthew Speir]

Hi Marco,

Thank you for your question about the difference between the GENCODE Basic and Comprehensive annotation sets. As you noted, the Basic annotation set is a subset of the Comprehensive set. GENCODE describes this Basic annotation set as:

What is the "basic" annotation in the GTF/GFF3?

The transcripts tagged as "basic" form part of a subset of representative transcripts for each gene. This subset prioritises full-length protein coding transcripts over partial or non-protein coding transcripts within the same gene, and intends to highlight those transcripts that will be useful to the majority of users.

from here: http://www.gencodegenes.org/faq.html. The GENCODE track description page also contains information on the selection criteria used for this Basic annotation set here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV22#basicSetSelection.

If you have questions about these selection criteria, I would recommend contacting GENCODE at http://www.gencodegenes.org/contact.html.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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