Questions tagged [ucsc]
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30 questions
2 votes
2 answers
102 views
Where can I get hg38 Copy number Variation (CNV) file?
I'm wondering how can I get standard hg38 Copy number Variation (CNV) file from UCSC website. Although, I got a link that is not working: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/encodeDCC/...
- 329
4 votes
2 answers
164 views
How to convert bed to wig file!
I was wondering how can I convert bed file to wig file. I have several bed files which look like ...
- 329
2 votes
0 answers
39 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 ...
- 43
1 vote
0 answers
71 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, ...
- 51
3 votes
0 answers
69 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: ...
- 343
1 vote
0 answers
25 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: ...
- 111
6 votes
2 answers
92 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?
- 646
2 votes
1 answer
113 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"...
- 21
-1 votes
1 answer
452 views
What's the meaning of Txn factor?
The transcription factor track in UCSC is named as Txn factor. Why Txn == Transcription?
- 113
0 votes
1 answer
141 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 ...
0 votes
1 answer
600 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 ...
1 vote
1 answer
149 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 ...
- 85
4 votes
1 answer
120 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 ...
- 365
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. ...
- 371
2 votes
1 answer
89 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. ...
- 3,204