User: Matthew_UCSC

gravatar for Matthew_UCSC
Matthew_UCSC20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
2 years, 4 months ago
Joined:
6 years, 1 month ago
Email:
m*****@soe.ucsc.edu

Posts by Matthew_UCSC

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
... Hi! Current UCSC Genome Browser staff member here. For number 5, we do actually import coordinates for some gene tracks, such as GENCODE for hg38 and mm10 or the Ensembl Gene tracks for assemblies other than those two. You are correct, though, that for a long time we did actually realign RNA sequen ...
written 3.3 years ago by Matthew_UCSC20
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Comment: C: GRCh37/38(NCBI) vs hg19/hg38(UCSC)
... The UCSC Genome Browser just released an "NCBI RefSeq" track that is based entirely on coordinates and alignments provided by the RefSeq group. These new tracks should avoid the issue of genes mapping to multiple locations, etc. You can read about it more on our website: https://genome.ucsc.edu/gold ...
written 3.3 years ago by Matthew_UCSC20
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Comment: C: uploading data in UCSC Microbial genome browser
... Yeah, that appears to be an issue with the Microbial Browser. You should contact Todd Lowe to bring this to his attention: http://lowelab.ucsc.edu/contact.html. The Genome Browser (https://genome.ucsc.edu) and the Microbial Browser (http://microbes.ucsc.edu/) are run by two different groups. The Ge ...
written 3.5 years ago by Matthew_UCSC20
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Comment: C: uploading data in UCSC Microbial genome browser
... That's true, but they are both based on the same software and so the pages on the UCSC Genome Browser's main site should be relevant to the Microbial Genome Browser. (Though I believe that the Microbial Browser is a few versions behind the main UCSC Genome Browser.) Here are the same pages on the M ...
written 3.5 years ago by Matthew_UCSC20
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Answer: A: uploading data in UCSC Microbial genome browser
... You cannot directly upload binary files, such as bigWig, bigBed, or BAM, directly to the Genome Browser. If you want to use bigWig then you must place the file on a publicly-accessible web server and then provide the URL to that location to the Genome Browser. See the bigWig format page: https://gen ...
written 3.5 years ago by Matthew_UCSC20

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