Questions tagged [genome-browser]
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Command line based interaction with the UCSC genome browser, automated data upload and track generation
Is there a way to submit data to ucsc genome browser for result/track display, on the fly, as a local bedgraph file with example contents like below: ...
How to display novel genome assemblies or uncommon genome assemblies using the UCSC Genome Browser?
I want to display E.coli BW25113 (GenBank: CP009273.1) strain in UCSC browser. This strain is not listed in http://microbes.ucsc.edu/ browser. How can I display E.coli BW25113 assembly in the browser?
Distinguishing Splicings that Produce Functional Transcripts Amongst Alternates Shown
This is a link to the UCSC Genome Browser showing a portion of Ch 17 containing TP53 here. There are several representations of the gene of varying length and number of exons. I presume these are ...
How are positions visually indicated in the UCSC Genome Browser?
I'm a little confused about how the position indices work in the browser. Based on the picture below, is base number 755440 an A or a ...
Syntenic gene browser
I found that there is a Syntenic gene browser at GEvo. Do anyone know where could I find a similar browser for a local installation?
Get gene exons from UCSC browser by HGNC name
I have a set of gene names in HGNC standard and I want to get all their exons (in BED format) from the UCSC browser but it seems like the browser doesn't index genes by their HGNC name. How can I do ...
Hba-a2 has two copies on UCSC genome browser
I was browsering the UCSC viewer of the genome at this region. UCSC genes label two genes as Hba-a2 while GENCODE thinks the left one is Hba-a1 Which annotation is correct?
How to get UCSC Genome Browser to show the actual sequence?
Is it possible to make UCSC Genome Browser to show the sequence (nucleotide chain) of the current region? I fiddled with the various viewing options and couldn't figure it out.
Customizing bigWig file
I generate bigWig files using bamCoverage from deeptools, in part for my colleagues to visualize their mapped libraries in the IGV viewer. A problem is that the ...