Frequently Asked Questions: Data and Downloads


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Downloading sequence and annotation data



You can download sequence and annotation data using our FTP server, but we recommend using rsync, which has the advantage of starting up where it left off after a failure, when run again. Please see the previous link for examples.



Another option for querying sequence and annotation data is the REST API. This interface allows for extraction of sequence and annotations from both UCSC assemblies and from hubs.

To quickly download large volumes of data you can use UDR (UDT Enabled Rysnc): UDR provides users much faster download rates. Here is an example using UDR, once installed, to download all the mouse mm9 ENCODE information that amounts to several terabytes:

$ udr rsync -avP /my/local/mm9/
$ udr rsync -avP /my/local/mm9/

Optional: download from our secondary download server.

$ udr rsync -avP /my/local/mm9/
Please read more about the new UDR method here.

Metadata tables for GenBank and RefSeq moved to hgFixed database

I can no longer find metadata tables like gbCdnaInfo for an assembly.

As of June 2016, the location of metadata tables that support the GenBank and RefSeq tracks (RefSeq, Other RefSeq, mRNA, EST, etc.) have been moved from directories of individual assemblies to one global database, hgFixed.

The tables below (previously found per assembly) can now be downloaded from the hgFixed database:

  • author
  • cds
  • cell
  • description
  • development
  • gbCdnaInfo
  • gbExtFile
  • gbLoaded
  • gbMiscDiff
  • gbSeq
  • gbWarn
  • geneName
  • imageClone
  • keyword
  • library
  • mrnaClone
  • organism
  • productName
  • refLink
  • refSeqStatus
  • refSeqSummary
  • sex
  • source
  • tissue

These tables are also accessible from:

Extracting sequence in batch from an assembly






Downloading data from the UCSC DAS server

How do I download data using the UCSC DAS server?




For example, here is a query that returns all the records in the refGene table for the chromosome position chr1:1-100000 on the hg16 assembly:,100000;type=refGene


A more recent alternative to the DAS server is the REST API.

Downloading the UCSC Genome Browser source

Where can I download the Genome Browser source code and executables?


See Downloading Blat source and documentation for information on Blat downloads.

Download restrictions




Opening .fa files


Microsoft Word or any program that can handle large text files will do. Some of the chromosomes begin with long blocks of Ns. You may want to search for an A to get past them.


Data differences between downloaded data and browser display

I downloaded the genome annotations from your MariaDB database tables, but the mRNA locations didn't match what was showing in the Genome Browser. Shouldn't they be in synch?


Strange characters in FASTA file



Symbol       Meaning      Nucleic Acid
   A            A           Adenine
   C            C           Cytosine
   G            G           Guanine
   T            T           Thymine
   U            U           Uracil
   M          A or C
   R          A or G        Purine
   W          A or T
   S          C or G
   Y          C or T        Pyrimidine
   K          G or T
   V        A or C or G
   H        A or C or T
   D        A or G or T
   B        C or G or T
   X      G or A or T or C
   N      G or A or T or C 

Selection of GenBank ESTs







EST strand direction


I want to confirm the strand assignment for two human ESTs:






gt/ag introns minus ct/ac introns = intronOrientation


Missing RefSeq ID

Why isn't my refseq ID in your database?

It may have been added after we last downloaded data from GenBank, or it may have been replaced or removed. You can check the submission date and status of an accession on the NCBI Entrez Nucleotide site.

Finished vs. draft segments




chr_alt chromosomes

What is chr_alt?

The chr_alt chromosomes, such as chr5_KI270794v1_alt, are alternative sequences that differ from the reference genome currently available for a few assemblies including danRer11, hg19, and hg38. These are regions of the genome that exhibit sufficient variability to prevent adequate representation by a single sequence. UCSC labels these haplotype sequences by appending "_alt" to their names. These alternative loci scaffolds (such as KI270794.1 in the hg38 assembly, referenced as chr5_KI270794v1_alt in the browser), are mapped to the genome and provide suppemental genomic information on these variable locations. To find the regions these alternate sequences correspond to in the genome you may use the Alt Haplotypes track if one is available.

Additional information on alternative loci can be found on our hg38 patches blog post as well as the Genome Reference Consortium (GRC) website.

chr_fix chromosomes

What is chr_fix?

The chr_fix chromosomes, such as chr1_KN538361v1_fix, are fix patches currently available for the hg19 and hg38 assemblies that represent changes to the existing sequence. These are generally error corrections (such as base changes, component replacements/updates, switch point updates or tiling path changes) or assembly improvements (such as extension of sequence into gaps). These fix patch scaffold sequences are given chromosome context through alignments to the corresponding chromosome regions. A list of all chromosomes including chr_fix sequences can be found in the hg19 or hg38 assembly sequences pages.

More information on these patch sequences can be found on our hg38 patches blog post as well as on the the Genome Reference Consortium (GRC) website.

chrN_random tables





Chromosome Un

What is chrUn?


Chromosome M

What is chromosome M (chrM)?

Mitochondrial DNA.

N characters at beginning of human chr22

When I download human chr22 from your web site, the unzipped file contains only Ns.

There is a large block of Ns at the beginning and end of chr22. Search for an A to bypass the initial group of Ns.

Erroneous duplicated chrY_random region on Mouse Build 34 (mm6)




Mapping chimp chromosome numbers to human chromosomes numbers

How do the chimp and human chromosome numbering schemes compare?


Human Chr Chimp Chr (panTro1) Chimp Chr (panTro2)
2 (part)122a
2 (part)132b

Converting genome coordinates between assemblies


You can migrate sequences from one assembly to another by using the Blat alignment tool or by converting assembly coordinates. There are two conversion tools available on the Genome Browser web site: the Convert utility and the LiftOver tool. The Convert utility, which is accessed from the View menu on the Genome Browser annotation tracks page, supports forward, reverse, and cross-species conversions, but does not accept batch input. The LiftOver tool, accessed via the Tools link on the Genome Browser home page, also supports forward, reverse, and cross-species conversions, as well as batch conversions.

If you wish to update a large number of coordinates to a different assembly and have access to a Linux platform, you may find it useful to try the command-line version of the LiftOver tool. The executable file for this utility can be downloaded here. LiftOver requires a pre-generated over.chain file as input, available for selected assemblies from the Downloads page. If the desired file is not available, send a request to the genome mailing list and we may be able to provide you with one.

Here is an example on how to set up and run LiftOver from the command line:

  1. Download the LiftOver program for your computer's operating system here
  2. Change permissions on that file so that it can be executed
    chmod +x liftOver
  3. Run the program with no arguments to see the usage statement
    liftOver - Move annotations from one assembly to another
       liftOver oldFile map.chain newFile unMapped
  4. Download your genome conversion chain file from the downloads directory. For example, the human to mouse conversion (hg38ToMm10) can be downloaded like so:
  5. Prepare your BED file input. Here is a few lines from a BED file you can copy into a text file, saved as "preLift.bed".
    chr1	11166587	11191615	MTOR
    chr9	136130562	136150630	ABO
    chr12	25358179	25403854	KRAS
    chrX	151335633	151619831	GABRA3
  6. You can now use the following command to LiftOver a BED file with annotations in your original genome, "preLift.bed", with your successful conversions in "conversions.bed" and unsuccessful conversions in "unMapped".
    ./liftOver preLift.bed hg19ToHg38.over.chain.gz conversions.bed unMapped

Linking gene name with accession number



Obtaining a list of Known Genes




Repeat-masking data




Availability of repeat-masked data

Are the repeat annotation files available for every chromosome?


RepeatMasker version differences - UCSC vs. RepeatMasker website



Obtaining promoter sequence

How can I fetch promoter sequence upstream of a gene?






Data from Evolutionary Conservation Score tracks



Minus strand coordinates - axtNet



start = chromSize + 1 - axtEnd
end = chromSize + 1 - axtStart

See an explanation of coordinate transforms in the genomeWiki.

Mapping UCSC STS marker IDs to those of other groups



deCODE map data

Where can I get more information about the deCODE map?


Direct MariaDB (MySQL) access to data


Yes. See our documentation on Downloading Data using MariaDB (MySQL).

Connect to the US MariaDB server using the command:

mysql --user=genome -A 

Or to the European MariaDB server using the command:

mysql --user=genome -A 

Name of fourth column in BED output

When using the Table Browser to extract exons from a Gene track, what does the "Name" column (fourth BED column) refer to?



This information is represented as follows:


Track Data Access

How do I access the data underlying a track?

The raw data underlying a track can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server, one of our two public MariaDB servers, or using our REST API.

bigBed data: For bigBed files, individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range using one of the hgdownload servers, example:

Read more in our blog about Accessing the Genome Browser Programmatically to acquire data.

How do I download dbSNP data?

For versions dbSNP153 and above, the data is formatted in bigBed files. Previous versions are MySQL tables. For help with versions before dbSNP153, see accessing MySQL data. This FAQ entry pertains to versions dbSNP153 and above.

Since dbSNP has grown to include over 700 million variants, the size of the All dbSNP (153+) subtrack can cause the Table Browser and Data Integrator to time out, leading to a blank page or truncated output, unless queries are restricted to a chromosomal region or to a specific set of rs# IDs (which can be pasted/uploaded into the Table Browser), or to one of the subset tracks such as Common or ClinVar.

For automated analysis, the track data files can be downloaded from the downloads server for hg19 and hg38. Below are specific examples for dbSNP153, however, the same methods and directories will work by substituting a more recent dbSNP release.





Example: retrieve variant rs6657048

bigBedNamedItems rs6657048 stdout

Example: retrieve all variants with rs# IDs in file myIds.txt

bigBedNamedItems -nameFile myIds.txt dbSnp153.myIds.bed


UCSC has an API that can be used to retrieve values from a particular chromosome range. A list of rs# IDs can also be pasted/uploaded in the Variant Annotation Integrator tool in order to find out which genes (if any) the variants are located in, as well as functional effect such as intron, coding-synonymous, missense, frameshift, etc.

See our searchable mailing list archives for more information and example queries. We also have information on our blog about Accessing the Genome Browser Programmatically to acquire data.

Obtaining GTF (Gene Transfer Format)

What is the best method for obtaining GTF output?

Currently, the Table Browser option return data in GTF format is limited as explained below. To convert custom GenePred format data into GTF, the best method is to use the command-line format conversion utility, genePredToGtf. This can optionally be set up to automatically connect to the UCSC public SQL database and return GTF files in a few minutes using this short guide.

For simplicity, GTF files have been generated using the genePredToGtf method described above and are available on our download server for the main gene transcript sets. These can be found at the following download server address:$db/bigZips/genes/ where $db is the assembly of interest. For example, the hg38 GTF files.

Summary of Table Browser limitations:

GenePred (short for Gene Predictions) is a table format commonly used for gene tracks in the UCSC Genome Browser where each transcript has a single row. Tables are not stored in GTF as it would require many rows to describe a single transcript since each gene feature (i.e., exon) requires a separate line. The genePredToGtf command-line utility can be used to convert genePred to GTF. Download the genePredToGtf operating system-specific command-line utility from the utilities directory.

Please see the Genes in GTF or GFF Format wiki page for examples and various methods for conversion. The genePredToGtf utility can convert files from several sources, such as Table Browser output from a genePred table, a local downloaded gene set table like refGene.txt, or from querying public MariaDB tables.

Table Browser output file order

My table browser output file is not ordered by position, how is it ordered?

Most of our tables have a special first column called "bin" that helps with quickly displaying data on the Genome Browser. This (chrom,bin) index causes query results to be ordered first by bin, then by chromStart. This allows us to query and return results more quickly than if they were sorted by chromStart.

A quick way to sort an output BED file by position is to use the following UNIX command on our Table Browser output BED file:

sort -k1,1 -k2n,2n example.bed > example.sorted.bed

'Permisssion denied' error when trying to use command-line utilities

Why do I get a 'Permission denied' error when I try to run command-line utilities?

In order for your computer to run a freshly downloaded utility, you will need to update the file system permissions to allow your operating system to run the program.
To make utilities usable, turn on its 'executable' bit:

 $ chmod +x ./filePath 
 $ ./filePath/utility_name
$ chmod +x /home/user/liftover/liftOver
See also:

Restricted Track Data

Why can I not download some data in the Table Browser or find the download files?

Some data is provided by external groups and is not available for download or mirroring by any third party without the permission of the owners, such as the OMIM track data, which is the property of Johns Hopkins University. For some tools, such as attempting a getData fetch with our API of restricted tracks, a 403 'Forbidden' error will be returned. Please email our private internal mailing list if you have any questions.

Analysis set

Some genomes in the download server also reference an analysis set, what is the difference?

For certain genomes (GRCm38/mm10, GRCh37/hg19, GRCh38/hg38), NCBI provides an analysis set in addition to the standard genome files. These are FASTA files with modified sequence identifiers and index files convenient for analysis with Next Generation Sequencing tools. These files are particularly helpful for NGS pipelines including variant calling and RNA-Seq analysis.

Though not all analysis sets contain the same information, features include:

For more information on analysis sets, see the NCBI FAQ. Information on what is contained in each specific assembly analysis set can be found in the README by clicking the Genome sequence files link for the assembly of interest in our Downloads page.