Questions tagged [genome-browser]
The genome-browser tag has no usage guidance.
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How come bigWigSummary shows coverage greater than 1 for some region of the genome?
I am running this command, using the UCSC utilities:
bigWigSummary -type=coverage ./galGal6.phastCons77way.bw chr4 25526708 25528708 1
to get phastCons77way ...
- 43
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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:
...
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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?
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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 ...
user7271
5
votes
1
answer
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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 ...
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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?
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85
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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 ...
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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?
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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.
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1
answer
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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 ...
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