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Questions tagged [ucsc]

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1answer
38 views

Accessing UCSC genome via ssh results in a validation error

I am working on macOS High Sierra. I am following the steps described here to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the ...
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0answers
26 views

Question: UCSC hub: autoscale option for multiwig track

I am making a hub on UCSC Genome Browser and I am aiming to display multiple bigWig files as a single track (multiwig container). I decided to use the autoscale option because I wanted a dynamic scale:...
2
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1answer
34 views

Finding URL for UCSC data hub

I am trying to build a UCSC track hub (a private one). I have all my hub files on a university server in a simple folder called /hub. I am using Ubuntu 16.04 and the server is also Ubuntu (16.04.3 ...
0
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1answer
32 views

Does the galGal5 chicken assembly have a chromosome 29?

The chromosome sizes at UCSC don't seem to contain chr29: ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal5/bigZips/galGal5.chrom.sizes It has a chr28 and a chr30. Am I missing something or is there ...
0
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1answer
34 views

differentially expressed intron analysis?

I have used Deseq for estimating the differentially expressed introns for the RNA seq data using the UCSC intron bed file. can Deseq be used for differentially expressed intron analysis?
5
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1answer
61 views

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 ...
1
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1answer
25 views

Link to UCSC gtexGene track description page for selected gene symbol

I have this link that comes up when I am in the browser window and click on the gene name, which leads me to description page about the gene (in this example it is BOK gene). How can I generate that ...
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2answers
43 views

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 ...
1
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1answer
23 views

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?
1
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1answer
89 views

How can I download genePred file from UCSC?

I need a gtf annotation file. UCSC doesn't give us a proper gtf file with distinct gene_id and transcript_id. It asked us to get a genePred file to convert to gtf. But where can we get genePred files?...
5
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1answer
162 views

Where to download JASPAR TFBS motif bed file?

I am interested in determining if any transcription factor binding site motifs are enriched in some BED files from a DNA methylation experiment. I am looking for a database that has BED Files ...
4
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1answer
176 views

Get canonical transcript from UCSC

I am using the following command to get all refseq genes from UCSC: ...