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: ...
Zebra Fish's user avatar
6 votes
2 answers

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 browser. How can I display E.coli BW25113 assembly in the browser?
Supertech's user avatar
  • 534
2 votes
1 answer

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 ...
user avatar
5 votes
1 answer

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 ...
Paghillect's user avatar
3 votes
1 answer

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?
user977828's user avatar
1 vote
2 answers

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 ...
Paghillect's user avatar
1 vote
1 answer

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?
Code42's user avatar
  • 282
3 votes
3 answers

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.
Paghillect's user avatar
5 votes
1 answer

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 ...
bli's user avatar
  • 3,070