Questions tagged [ucsc]

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7 votes
1 answer
2k 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 ...
Reilstein's user avatar
  • 367
6 votes
2 answers
51 views

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?
Supertech's user avatar
  • 596
5 votes
1 answer
76 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 ...
Paghillect's user avatar
4 votes
1 answer
492 views

Get canonical transcript from UCSC

I am using the following command to get all refseq genes from UCSC: ...
terdon's user avatar
  • 9,846
4 votes
1 answer
92 views

Where can I find lncRNA expression data for different cell types?

Are there any publicly available databases providing expression data for long non-coding RNAs (lncRNAs) across cell types of multicellular organisms? Alternatively, are there lesser known UCSC tracks ...
Gawain's user avatar
  • 315
3 votes
1 answer
114 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 ...
mf94's user avatar
  • 203
3 votes
0 answers
50 views

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
2 votes
1 answer
65 views

Efficiently concatenating disjoint, ordered bigBed files

Given a set of bigBed files, each of which are disjoint to each other and in lexicographical ("sort-bed") sort order, I would like to know if there is a way to concatenate these archives efficiently. ...
Alex Reynolds's user avatar
2 votes
1 answer
35 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 ...
zx8754's user avatar
  • 1,042
2 votes
1 answer
75 views

Hg38 annotation tracks retrieval

I want to retrieve an annotation object (as GRanges) containing different UCSC annotation tracks such as CpG Islands, TSS, TFBS and promoters for hg38 Human reference genome. But "UCSC Genes"...
TRakesh's user avatar
  • 21
2 votes
1 answer
103 views

UCSC liftover cannot produce bed format output

I was trying to use UCSC liftover tool to convert human coordinates to mouse. While most of the files worked, one file didn't: ...
Code42's user avatar
  • 282
2 votes
0 answers
21 views

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 ...
VeritatemAmo's user avatar
1 vote
2 answers
88 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 ...
Paghillect's user avatar
1 vote
1 answer
2k views

How to visualize called narrowPeak files in UCSC Genome browser or IGV?

I have called peaks using MACS2. Then I got a narrowPeak file like this. ...
MudithMMBc's user avatar
1 vote
1 answer
152 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 ...
Biomagician's user avatar
  • 2,459
1 vote
1 answer
34 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?
Code42's user avatar
  • 282
1 vote
1 answer
498 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?...
Code42's user avatar
  • 282
1 vote
0 answers
53 views

ucsc-bedgraphtobigwig throwing memory allocation error

I installed the latest ucsc-bedgraphtobigwig (v377) with conda in a new enviroment enviroment inmy WSL2. conda install -c bioconda ucsc-bedgraphtobigwig However, ...
ricardo3889's user avatar
1 vote
0 answers
17 views

Running hubCheck utility from inside K8s's Pod

I'm trying to run hubCheck utility* from inside Kubernetes Pod but for some reason I get this Network error: ...
Bilal's user avatar
  • 111
1 vote
0 answers
140 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:...
mf94's user avatar
  • 203
0 votes
1 answer
171 views

What is the `table` parameter in the UCSU ldHgGene tool?

I want to lift over the annotation from E. coli release 29 to E. coli release 42. I have followed the steps for an annotation liftover mentioned here. I got the chain file for the final step and ran: ...
Biomagician's user avatar
  • 2,459
0 votes
1 answer
420 views

How to visualize called narrowPeak files in UCSC Genome browser? [closed]

I have this file: and I get this error I googled and found this solution but it still doesn't work and I get this error Error File 'GSM2797523_FOXA2_IDR0.02_narrowPeak_try.bed' - line 1 of custom ...
Libby Kosolapov's user avatar
0 votes
1 answer
103 views

How to annotate gene length to a list of gene symbols using UCSC data?

I have a list of HGNC gene symbols, I am looking to get the gene length of each gene. Although I also describe these genes with lots of UCSC datasets as features, so I am wondering if there is a ...
DN1's user avatar
  • 45
0 votes
1 answer
205 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 ...
juniper-'s user avatar
  • 890
0 votes
1 answer
106 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?
jagat shrestha's user avatar
0 votes
1 answer
90 views

How can I add for several bed files the header : track type=narrowPeak name=“narrowPeak” preferably in python ,can handle with R

I want to create custom tracks from these files I can add the line : track type=narrowPeak name=“narrowPeak” manually by opening it with text editor: track type=narrowPeak name=“narrowPeak” but I ...
Libby Kosolapov's user avatar
0 votes
1 answer
213 views

UCSC packages/tools ucsc-netchainsubset and ucsc-fatotwobit not working on GNU/Linux

I have installed some ucsc tools on my Mac computer and it worked fine: Installation ...
Biomagician's user avatar
  • 2,459
-1 votes
1 answer
301 views

What's the meaning of Txn factor?

The transcription factor track in UCSC is named as Txn factor. Why Txn == Transcription?
Jie's user avatar
  • 113