Latest assembly of Nile tilapia/ ASM185804v2/ BED annotation file
Tomasz Krzysztof Podgorniak
Hello,
I would like to know if you are planning to add to the UCSC Table Browser the annotation data for the last assembly of Nile tilapia genome ( Oreochromis niloticus, 2016, ASM185804v2, https://www.ncbi.nlm.nih.gov/assembly/GCF_001858045.1/ ).
Indeed, UCSC currently provides the annotation BED file of a poorer assembly (orenil1.1/orenil2), whereas NCBI provides only a GFF3 file of ASM185804v2.
The conversion of GFF to BED12 standard (via Galaxy or BEDOPS) doesn’t seem to work for that file.
Thanks in advance,
Cheers,
Tomasz PODGORNIAK
Post-doc in EPIFISH Project
Epigenetics of fish domestication
Faculty of Biosciences and Aquaculture (FBA)
Group of Aquaculture Genomics
Nord University, Norway
Office: +47 75517448
email:
tomasz.p...@nord.no
Cath Tyner
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Cath Tyner
Tomasz Krzysztof Podgorniak
Hello,
Thank you for the GFF ->BED12 conversion.
However, when I tried to use the orenil3 BED file I realized that it contains only 181 genetic sequences..
Is it due to some selection process during the conversion or is it a consequence of incorrect original GFF file?
I have also verified the official UCSC annotation file of the previous version of tilapia genome (orenil2/1.1),
it has also a very small number of genes (ca.190).
Thank you in advance,
Tomasz PODGORNIAK
Post-doc in EPIFISH Project
Epigenetics of fish domestication
Faculty of Biosciences and Aquaculture (FBA)
Group of Aquaculture Genomics
Nord University, Norway
Office:
+47 75517448
email:
tomasz.p...@nord.no
From: Cath Tyner [mailto:ca...@ucsc.edu]
Sent: Thursday, August 3, 2017 9:09 PM
To: Tomasz Krzysztof Podgorniak <tomasz.p...@nord.no>
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] Latest assembly of Nile tilapia/ ASM185804v2/ BED annotation file
Hello Tomasz,
Thank you for contacting the UCSC Genome Browser support team. We have added the 2016 GCF_001858045.1 assembly for Oreochromis niloticus for you to access on our development server for oreNil3. In the future, this assembly will eventually be processed for quality control and will be available on our production server. For now, you can select the oreNil3 assembly in the Table Browser at the development site.
clade: Vertabrate
genome: Nile tilapia
assembly: oreNil3
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Cath
Brian Lee
Dear Tomasz,
Thank you for using the UCSC Genome Browser and your question about the number of entries for the oreNil3 database on our development server.
The refGene track for oreNil3, http:/genome-test.soe.ucsc.edu/cgi-bin/hgTrackUi?db=oriNil3&g=refGene, is taken from the NCBI RNA reference sequences collection and hence is limited to the number of entries they currently have available. If you click an item like NM_001279455.1, you will arrive at the corresponding source at https://www.ncbi.nlm.nih.gov/nuccore/NM_001279455?report=GenBank and find an "ORIGIN" section where the sequence displays that was used to create the track Because this track is limited to what mRNA have been accessioned and are available at GenBank, it means at the current time there are less than 200 entries to display, although they are spread across a variety of chromosomes.
To increase your output you can use the other gene prediction tracks. There is the augustusGene table with 59,530 items (http:/genome-test.soe.ucsc.edu/cgi-bin/hgTrackUi?db=oriNil3&g=augustusGene), and the genscan table with 35,445 items (http:/genome-test.soe.ucsc.edu/cgi-bin/hgTrackUi?db=oriNil3&g=genscan)and lastly the xenoRefGene table that attempts to align GenBank data from other organisms with 143,293 items (http:/genome-test.soe.ucsc.edu/cgi-bin/hgTrackUi?db=oriNil3&g=xenoRefGene).
Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Brian Lee
UCSC Genomics Institute
Hello,
Thank you for the GFF ->BED12 conversion.
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Cath
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