Hello Guys,
I have analyzed a set of ChiP-seq data for a Transcription factor. I have my BigWig files and a list of genes names (ncRNA)...
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How do I convert a list of ncRNA genes into annotation using UCSC table browser
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Liftover dog canFam3 to human hg19
Hi my question is relatively simple. I've converted dog coordinates to human using UCSC LiftOver. These are 200bp intergenic regions that are differentially... -
Tutorial or documentation for using UCSC MySQL
Last edited by user 31888; 12-24-2015, 12:22 PM. -
Obtain a bed file with the name of gene
Hi,
I have a gene of interest. How can I obtain the bed file for the particular gene. I tried it on UCSC. Is there an alternate way? Is... -
byte range enabled server for NGS data?
I use the UCSC genome browser to view NGS data. The browser needs to point a url to a server where data is stored in a binary (bigWig) format. I’ve... -
calculations of tophat BlockSizes and BlockStarts
Hi,
I know it has been discussed here a few times, but no one really explain how it is done.
I have this example of a tophat...Last edited by frymor; 10-08-2014, 08:52 AM. -
How to get TCGA transcript isoforms sequences ?
Hi all,
I've downloaded the breast cancer RNA-seq2 data from TCGA. it's contain the isoform of the genes .
I'm looking way to get...Last edited by watermark; 02-25-2014, 08:04 AM. -
DNA Sequences indexed by Bing.com
UCSC GenomeBrowser now hosts tracks of DNA sequences extracted from Bing web crawl mapped to genome coordinates: http://genome.ucsc.edu/cgi-bin/hgTra... -
UCSC AXTCHAIN installation error
I am trying to install axtchain on my computer through the UCSC genome brower and I have MYSQL installed but I keep getting a error involving MYSQL library.... -
Why does UCSC genome browser NOT using spatial index?
UCSC genome browser uses binning strategy to retrieve genes more efficiently than simply creating a B-tree on the start and end coordinates. This certainly... -
UCSC human conservation data
I am using GenomeGraphs and want to plot conservation scores alongside human gene regions. In the vignette, they use yeastCons1. Where would I get the... -
Calculate mappability for an interval?
Hi all,
I downloaded the mappability file from here:
ftp://encodeftp.cse.ucsc.edu/pipelin...odeMapability/
then...Last edited by Vasilisa; 01-16-2013, 09:06 AM. -
Calculate mappability for an interval?
Hi all,
I downloaded the mappability file from here:
ftp://encodeftp.cse.ucsc.edu/pipelin...odeMapability/
...Last edited by Vasilisa; 01-16-2013, 07:10 AM. -
Obtain figures from UCSC
UCSC genome browser is powerful to visualize the sequence, alignment, etc. My question is how can I directly download those figures and other information... -
Over representation testing on repeat element subclass terms
Hi all,
I have UCSC tracks that after processing show subclass terms of a particular class of repeat elements.
Is there...
