[ensembl-dev] Refseq cache file

[Andrew Parton]

Hi Duarte,

There were no updates to our VEP cache transcript set for GRCh37 from e98 -> e99, so the files should still be the same.

Kind Regards,
Andrew 

> On 20 Apr 2020, at 11:33, Duarte Molha <duartemolha at gmail.com> wrote:
> 
> Many thanks
> 
> Good to know that going forward there will be a single source file.
> 
> Unfortunately right now we are using version 98 and will not be transitioning in the short term. 
> 
> Could you let me know the source ref files for version 98 cache?
> Are they the same as version 99 you listed?
> 
> Many thanks again
> 
> Duarte
> 
> 
> On Fri, 17 Apr 2020 at 17:42, Andrew Parton <aparton at ebi.ac.uk <mailto:aparton at ebi.ac.uk>> wrote:
> Hi Duarte,
> 
> Unfortunately we don’t have one GFF file that covers all transcripts within our GRCh37 cache files. Additionally, we will be providing significant updates to these files very soon.
> 
> For release 100, scheduled for release at the end of April, a new set of RefSeq transcripts are included within our GRCh37 cache files. They can be found here: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz <ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz>
> 
> As for release 99, the GRCh37 RefSeq cache contains 2 different RefSeq versions
> the last annotation on GRCh37 
> ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz <ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz>
> a GRCh38 annotation projected to GRCh37
> ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.109/GRCh37.p13_interim_annotation/ <ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.109/GRCh37.p13_interim_annotation/>
> 
> 
> If you would like to have a closer look at the exact data included within the RefSeq cache file, you can access our publicly available mysql database by following these instructions: https://www.ensembl.org/info/data/mysql.html <https://www.ensembl.org/info/data/mysql.html> - the homo_sapiens_otherfeatures_99_37 database contains the transcript sets included within our cache files.
> 
> Kind Regards,
> Andrew
> 
> 
> 
> 
>> On 16 Apr 2020, at 17:01, Duarte Molha <duartemolha at gmail.com <mailto:duartemolha at gmail.com>> wrote:
>> 
>> Dear Devs
>> 
>> I was wondering if you could help me with the source of the cache data for VEP
>> 
>> ON this link https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html <https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html>
>> 
>> you list the refseq source of the transcripts used to this file:
>> 
>> 
>> 2019-06-28
>> (GCF_000001405.39_GRCh38.p13_genomic.gff)
>> This is great but I am interested in also getting the correct source for the hg19 version
>> 
>> You have simply listed it as :
>> 
>> 2015-01
>> 
>> And I have not been able to match this date to any of the GCF files 
>> 
>> The latest I could find for GRCh37 is 
>> 
>> https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/ <https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/> 
>> 
>> but this file dates to   2013/06/28 
>> 
>> Can you please point me where I can get the 2015-01 refseq GFF source file you have used for the cache?
>> 
>> Best regards
>> 
>> Duarte
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