User: Luis Nassar

gravatar for Luis Nassar
Luis Nassar290
Reputation:
290
Status:
Trusted
Location:
UCSC Genome Browser
Website:
http://genome.ucsc.edu...
Last seen:
1 day, 2 hours ago
Joined:
1 year ago
Email:
v*****@gmail.com

Posts by Luis Nassar

<prev • 27 results • page 1 of 3 • next >
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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 8 days ago by Luis Nassar290
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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 8 days ago by Luis Nassar290
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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 8 days ago by Luis Nassar290
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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 6 weeks ago by Luis Nassar290
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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 6 weeks ago by Luis Nassar290
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Answer: A: Understanding the annotation tag
... Hello, We have an FAQ entry (albeit a bit hidden) on this question: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download34 The fourth column of the BED output contains a lot of information separated by underscores. For example: uc009vjk.2_cds_1_0_chr1_324343_f This information is represented as ...
written 6 weeks ago by Luis Nassar290
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Answer: A: UCSC Genome Browser GENCODE Subtrack Label Highlighted?
... Hello, This highlighting is representing something different than the track display, which we may not be very clear about. What the highlighting in this case is showing is the transcript you selected from your search results. You probably got here by [searching for TP53][1] . If you click the firs ...
written 6 weeks ago by Luis Nassar290
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Answer: A: GEO database - how to use their bedgraph files
... Hello, To answer your first question regarding the correct Genome Browser, you will have to check the assembly used in GEO and see if we have the corresponding assembly for that organism as a native assembly. You can see this in the organism gateway page, e.x. https://genome.ucsc.edu/cgi-bin/hgGate ...
written 12 weeks ago by Luis Nassar290
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Comment: C: Sequence mapping with reciprocal-best but not liftover chains?
... If you could send your question as an email to our help desk (genome@soe.ucsc.edu) we can take a look. If you could also include examples of sequences mapping as orthologs in the reciprocal-best but not the liftover chains that would be helpful. ...
written 4 months ago by Luis Nassar290
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Answer: A: What does arrow+box mean in UCSC genome browser?
... The arrow+box (which we refer to as double horizontal lines) represents an alignment with gaps in both the target genome and the query sequence. There are three ways the alignment can be drawn in BLAT results: - **Solid black bar**: The query matches the genome entirely in that region. - **Sin ...
written 4 months ago by Luis Nassar290

Latest awards to Luis Nassar

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 7 days ago, created an answer that has been accepted. 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 4 months ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 8 months ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 9 months ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 9 months ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 9 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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