Missing Lamprey Annotation Files

[mayur prag]

Good Day

I wanted to inform you that there are missing annotation (GTF/GFF) files for all the versions of the lamprey genomes on the genome browser.

Kind regards,

Mayur Prag

Hockman Lab

Department of Human Biology

University of Cape Town

[Brian Lee]

Dear Mayur Prag,

Thank you for using the UCSC Genome Browser and your question about annotation (GTF/GFF) files for lamprey (Petromyzon marinus - petMar1, petMar2, petMar3).

We do have this petMar2.ensGene.gtf.gz file here: http://hgdownload.soe.ucsc.edu/goldenPath/petMar2/bigZips/genes/

We do not generate these files for all assemblies and all gene sets. See this FAQ for more information: http://genome.ucsc.edu/FAQ/FAQgenes.html#gtfDownload

These files are generated for four gene model tables: ncbiRefSeq, refGene, ensGene, knownGene. Certain assemblies, such as hg19, will have all four files while smaller assemblies may only have one or two of these.

There are ways to generate more GTF files either from the Table Browser (with some issues) or of better quality with a utility called genePredToGtf as described in this FAQ: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download37

You may also be interested to learn therre is an assembly hub on lamprey available: https://genome.ucsc.edu/h/GCF_010993605.1

That hub has an NCBI RefSeq track where if you click into the track and then see the track description points to a source location for the GTF files.

The RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using data from the NCBI RefSeq project. GFF format data files were downloaded from the file GCF_010993605.1_kPetMar1.pri_genomic.gff.gz delivered with the NCBI RefSeq genome assemblies.

In this hub's case: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/993/605/GCF_010993605.1_kPetMar1.pri/

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Brian Lee

UCSC Genome Browser  

UC Santa Cruz Genomics Institute |  Revealing life’s code.

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