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5 votes
Accepted

How are positions visually indicated in the UCSC Genome Browser?

It's an A. The number refers to the position just before the |. This is clearer on different zoom levels, but I double checked by going to the very beginning of a ...
terdon's user avatar
  • 9,826
4 votes

How to display novel genome assemblies or uncommon genome assemblies using the UCSC Genome Browser?

I found two methods: You want to visit this page for instructions for novel assemblies: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs . However, before doing that I highly recommend that you ...
Supertech's user avatar
  • 596
3 votes
Accepted

Where to download JASPAR TFBS motif bed file?

You could make your own such file with FIMO, the JASPAR MEME files available via the MEME download site, and your genome build of interest (per-chromosome FASTA files from UCSC goldenpath, say), e.g., ...
Alex Reynolds's user avatar
3 votes
Accepted

Get canonical transcript from UCSC

You can link them with the kgXref table, since kgXref.refseq == refGene.name and ...
Devon Ryan's user avatar
  • 19.6k
3 votes
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What is the `table` parameter in the UCSU ldHgGene tool?

I stumbled across this issue after getting the same warning message from liftOver. By using the -out option of ...
knowah's user avatar
  • 46
2 votes
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Accessing UCSC genome via ssh results in a validation error

You need to setup ssh keys. All the commands in the script are going to use ssh to run the commands. Note the tips here of how to setup ssh keys: http://genomewiki.ucsc.edu/index.php/...
Null Model's user avatar
2 votes
Accepted

Finding URL for UCSC data hub

Check your webserver functions from the top down. You can do this from any WEB browser, even one that is on the webserver system itself. For example, does this link function: http://webserver-id/ ...
Null Model's user avatar
2 votes
Accepted

Does the galGal5 chicken assembly have a chromosome 29?

The current ensembl entry doesn't have a 29 either. The archived ensembl assembly lacks 29 30, and 31 and 33 and LGE64. The chromosomes after 30 are tiny, so they might not be visible in a ...
swbarnes2's user avatar
  • 1,890
2 votes

differentially expressed intron analysis?

Typical tools to use for this would be the DEXseq packages (as done here) or rMATS, which will calculate intron retention rates. I would generally suggest not summing intronic counts by gene and ...
Devon Ryan's user avatar
  • 19.6k
2 votes
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Link to UCSC gtexGene track description page for selected gene symbol

You never want to include the hgsid parameter in your url because that is the link to your current browsing session and all its specific contents. So if you send that link to someone else and then ...
Christopher Lee's user avatar
2 votes

Get gene exons from UCSC browser by HGNC name

If you need a 3-column BED, you can just use standard Unix tools: ...
user172818's user avatar
  • 6,525
2 votes
Accepted

Get gene exons from UCSC browser by HGNC name

You could grab exons via Gencode v27 (hg38) GFF annotations and convert them to BED via BEDOPS convert2bed/gff2bed: ...
Alex Reynolds's user avatar
2 votes
Accepted

Hba-a2 has two copies on UCSC genome browser

Gencode is correct (when in doubt, always assume Gencode/Ensembl is correct when it differs from UCSC). What presumably happened is that the UCSC annotation pipeline noticed that Hba-a1 and Hba-a2 are ...
Devon Ryan's user avatar
  • 19.6k
2 votes

How to visualize called narrowPeak files in UCSC Genome browser?

Headers should not contain tabs: track type=narrowPeak name="Somite narrowPeak" description="Somite narrowPeak" Ensure that you have NO tabs on ...
Devon Ryan's user avatar
  • 19.6k
2 votes
Accepted

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

You could do a few command-line operations to answer this question. This assumes the use of hg38 assembly. First, get a list of genes from GENCODE: ...
Alex Reynolds's user avatar
2 votes

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

As long as the lncRNA is annotated you can use https://gtexportal.org/home/gene.
Mary Allen's user avatar
2 votes
Accepted

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

I think you might have changed the separator (or at least have some kind of inconsistency from the required format) for your file. Note that peak output files from MACS2 are variants of BED files. It ...
story's user avatar
  • 1,573
2 votes
Accepted

Efficiently concatenating disjoint, ordered bigBed files

No, there's no simple way to do that without someone writing a program tailored toward it that handles the footer section and recreates the zoom levels that follow the compressed blocks of intervals. ...
Devon Ryan's user avatar
  • 19.6k
1 vote

How to display novel genome assemblies or uncommon genome assemblies using the UCSC Genome Browser?

I am not sure if this qualifies as an official answer. I have contacted UCSC bioinformatics team. They were were very kind and told me that they would add any track that was requested by users. After ...
Supertech's user avatar
  • 596
1 vote

Hg38 annotation tracks retrieval

The UCSC Data Integrator can combine multiple tracks (CpG Islands, TFBS, cCREs, etc.) into one output annotation file, and it works with any assembly you choose. You can select which output fields you ...
ethan4444444's user avatar
1 vote

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

I don't think you need to go to R or Python to do that. In bash ...
Bastian Schiffthaler's user avatar
1 vote
Accepted

UCSC liftover cannot produce bed format output

I figured out the issue by myself. It turned out that UCSC liftover doesn't like the character ":" I removed ":" and it worked
Code42's user avatar
  • 282
1 vote

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

Short answer: respect the case of the tool name Longer story below Thanks to terdon, I printed the PATH when the conda environment was active and listed what was in the folder where conda installed ...
Biomagician's user avatar
  • 2,459
1 vote

How can I download genePred file from UCSC?

It turned out that using table browser on UCSC we could download an output with all fields. That output actually contains a GenePred file but has one extra column on the left end. The genePred file ...
Code42's user avatar
  • 282

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