User: Luis Nassar

gravatar for Luis Nassar
Luis Nassar360
Reputation:
360
Status:
Trusted
Location:
UCSC Genome Browser
Website:
http://genome.ucsc.edu...
Twitter:
@GenomeBrowser
Last seen:
5 days, 18 hours ago
Joined:
1 year, 2 months ago
Email:
v*****@gmail.com

Posts by Luis Nassar

<prev • 32 results • page 1 of 4 • next >
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Answer: A: RepeatMasker data download
... Hello, We have built assembly hubs for many assemblies (including goat), these include RM tracks: https://genome.ucsc.edu/h/GCF_001704415.1 That download data can be found in the following directory: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.1/bbi/ There you will see a fe ...
written 11 days ago by Luis Nassar360
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Answer: A: Local installation of UCSC Genome Browser
... Hello, As you have said, we have a few different options if you want a mirror installation. We recommend GBiB (https://genome.ucsc.edu/goldenPath/help/gbib.html) as the simplest method, it's a self-contained virtual machine containing a functional Genome Browser. GBiC is another solution, when you ...
written 26 days ago by Luis Nassar360 • updated 26 days ago by RamRS26k
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Comment: C: Quick way to annotate a target exome BED file with gene name information
... Are you looking for gene symbols (MTOR), or Ensembl identifiers (ENSG*)? We should be able to help you using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) or Data Integrator (http://genome.ucsc.edu/cgi-bin/hgIntegrator). There are also computational solutions using the mysql server or ...
written 5 weeks ago by Luis Nassar360
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Comment: C: How to download mm10 GTF file with the gene id and gene name using UCSC table br
... The difference is the dataset they were sourced from. You can read about these different tracks in the description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite). **ncbiRefSeq** - RefSeq All – all curated and predicted annotations provided by RefSeq. **refGene** - UCS ...
written 6 weeks ago by Luis Nassar360
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Answer: A: UCSC browser track description can't be updated
... Hello, The problem seems to be the passed attribute "desc". You can update the description of the custom track by using the "description" track line attribute. The attribute is case-sensitive and any misspellings will cause the attribute to be ignored by the Genome Browser. You can learn more abou ...
written 7 weeks ago by Luis Nassar360
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Comment: C: How to download mm10 GTF file with the gene id and gene name using UCSC table br
... Yes, we are still in the process of making them available for all of our assemblies. hg38 GTFs: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/ hg19 GTFs: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/ ...
written 11 weeks ago by Luis Nassar360
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Answer: A: How to download mm10 GTF file with the gene id and gene name using UCSC table br
... Hello, Short answer: http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/mm10.refGene.gtf.gz Long answer: Due to the way the Table Browser forms queries, the Table Browser GTF output repeats the gene_id and transcript_id fields as such: chr1 mm9_refFlat stop_codon 3206103 3206105 0.000 ...
written 11 weeks ago by Luis Nassar360
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Answer: A: Get GC content, Conservation score and repeat fraction from UCSC?
... Hello, These entire data sets are all available from our download server (as well as our API and public mysql for programmatic point access). Here is an example of the data locations for GRCh38/hg38: * GC content - http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/gc5BaseBw.txt.gz * conserva ...
written 11 weeks ago by Luis Nassar360
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Answer: A: Getting CDS from chromosome positions
... The UCSC Genome Browser may not be the most efficient tool to go from position coordinate to predicted effect via programmatic approach. We recently announced our API (http://genome.ucsc.edu/goldenPath/help/api.html) which does allow python access to coding sequence given coordinates, as well as qu ...
written 3 months ago by Luis Nassar360
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Answer: A: Locating telomere on a given chromosome
... Hello, Late to the party, but present non-the-less. This question has come up before in the Genome Browser: https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/telomere$20mm9|sort:date/genome/fN1dPsobIcg/8Vue9ImwKAAJ and we have a wiki entry on how to get gaps (https://genome.ucsc.edu ...
written 3 months ago by Luis Nassar360

Latest awards to Luis Nassar

Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 11 weeks ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 6 months ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 10 months ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 11 months ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 12 months ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?

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