User: Luis Nassar

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Luis Nassar110
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Posts by Luis Nassar

<prev • 15 results • page 1 of 2 • next >
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Comment: C: UCSC different exome sets per each gene
... Oh, I see, I believe I understand, you're looking for each of the individual exon start/stop for one isoform per gene? You're right, the knownCannonical table does not have exon start/stop coordinates. The following should work for you though: 1. Choose the knownCannonical table as described above ...
written 25 days ago by Luis Nassar110
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Comment: C: UCSC different exome sets per each gene
... Ah, in that case you can change the output to **BED** then **get output** and in the following page you will see: **Create one BED record per:** If you select **Coding Exons** (or **Exons plus 0** if you want to include UTR regions), you should get an output like such, with one entry for each exo ...
written 25 days ago by Luis Nassar110
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Answer: A: UCSC different exome sets per each gene
... As Pierre mentioned, knownGene includes a large set of transcripts, in total it has 82,960 items. If you are just looking for one representative transcript per gene, then I would recommend you use the knownCanonical table instead. This table is a subset of the knownGene, generally the longest isofor ...
written 25 days ago by Luis Nassar110
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Answer: A: Protein coding annotation from UCSC
... Hello Tim, With your same selections on the [Table Browser][1], if you change the **output format** to **BED**, you will see additional options to refine the output. The following page will say: **Create one BED record per:** Which by default makes an entry for the Whole Gene. You can instead des ...
written 28 days ago by Luis Nassar110
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Answer: A: How to zoom out to whole genome view in UCSC browser?
... Late to the party here, As far as your first question, we actually have a lesser known tool that I believe can do what you're asking. The Genome Graph (http://genome.ucsc.edu/cgi-bin/hgGenome) CGI will show you the density of objects located throughout the entire genome. You can import your ChIP-se ...
written 9 weeks ago by Luis Nassar110
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Comment: C: RefGene: how to find the starts and ends of genes?
... You can find all all the hg38 annotations including the ncbiRefSeq in our downloads directory: > http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ You can also do a MySQL query same as above, but instead of querying the refGene table, you can query ncbiRefSeq: $mysql -h genome-mysql ...
written 10 weeks ago by Luis Nassar110
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Answer: A: RefGene: how to find the starts and ends of genes?
... In most all cases what you are describing should work to find the start/end of the gene. The way we build the refGene track is to BLAT all the NCBI sequences ourselves, though we also offer a track with all the NCBI provided alignmend: ncbiRefSeq. All of the NR_* accession numbers are experimentall ...
written 10 weeks ago by Luis Nassar110
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Comment: C: Why the list of genes in UCSC "knownGene" table is strikingly different than the
... Hello Vijay, To get an output from the knownGene table like the one you described you will want to use the "selected fields from primary and related tables" option in the Table Browser: Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables assembly: hg19 track: UCSC Genes table: knownGene output ...
written 3 months ago by Luis Nassar110
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Comment: C: Why the list of genes in UCSC "knownGene" table is strikingly different than the
... I do, currently QA at UCSC Genome Browser. Our main support address is genome@soe.ucsc.edu, but we keep an eye on biostars when we can (the UCSC tag helps). ...
written 3 months ago by Luis Nassar110
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Answer: A: Why the list of genes in UCSC "knownGene" table is strikingly different than the
... Hello Vijay, What you are observing here with the missing BBS5 entry in the knownCanonical table is an artifact of how that table was created for hg19. If you take a look at the hg19 UCSC Genes description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene ) we define knownCanon ...
written 3 months ago by Luis Nassar110 • updated 3 months ago by genomax68k

Latest awards to Luis Nassar

Scholar 29 days ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: RefGene: how to find the starts and ends of genes?
Scholar 8 weeks ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
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?
Scholar 10 weeks ago, created an answer that has been accepted. For A: RefGene: how to find the starts and ends of genes?
Teacher 10 weeks 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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