• Downloading sequence and annotation data
• Extracting sequence in batch from an assembly
• Downloading data from the UCSC DAS server
• Downloading the UCSC Genome Browser source
• Download restrictions
• Opening .fa files
• Data differences between downloaded data and browser display
• Strange characters in FASTA file
• Selection of GenBank ESTs
• EST strand direction
• Missing RefSeq ID
• Finished vs. draft segments
• chrN_random tables
• Chromosome Un
• Chromosome M
• N characters at beginning of human chr22
• Erroneous duplicated chrY_random region on Mouse Build 34 (mm6)
• Problems with Mouse Build 32 (mm4)
• Mapping chimp chromosome numbers to human chromsomes numbers
• Converting genome coordinates between assemblies
• Linking gene name with accession number
• Obtaining a list of Known Genes
• Repeat-masking data
• Availability of repeat-masked data
• RepeatMasker version differences - UCSC vs. Repeatmasker website
• Obtaining promoter sequence
• Data from Evolutionary Conservation Score tracks
• Minus strand coordinates - axtNet files
• Mapping UCSC STS marker IDS to those of other groups
• deCODE map data
• Direct MySQL access to data

Question:
"How do I obtain the sequence and/or annotation data for a release?"

Response:
Sequence and annotation data downloads are usually made available within the first week of the release of a new assembly. The download directories are automatically updated nightly to incorporate additions and modifications to the data.

We recommend that you download data via our FTP site at ftp://hgdownload.cse.ucsc.edu/, particularly if you plan to download multiple files or files of large size. To do so:

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: your email address
    go to the goldenPath directory, pick an assembly directory, then a data directory

To download multiple files from the UNIX ftp command line, use the "mget" command. You may want to use the "prompt" command to toggle the interactive mode if you do not want to be prompted for each file that you download.

    mget [filename1] [filename2] ...

    - or -

    mget -a (to download all the files in the directory) 

You can also download data from our Downloads page or our DAS server. To download a specific subset of the data or to configure the output format of the data, use the Table Browser. For information on extracting a large set of sequences from an assembly, see Extracting sequence in batch from an assembly.

For more information on using the UCSC DAS server, see Downloading data from the UCSC DAS server.

Question:
"I have a lot of coordinates for an assembly and want to extract the corresponding sequences. What is the best way to proceed?

Response:

There are two ways to extract genomic sequence in batch from an assembly:

A. Download the appropriate fasta files from our ftp server and extract sequence data using your own tools or the tools from our source tree. This is the recommended method when you have very large sequence datasets or will be extracting data frequently. Sequence data for most assemblies is located in the assembly's "chromosomes" subdirectory on the downloads server. For example, the sequence for human assembly hg17 can be found in ftp://hgdownload.cse.ucsc.edu/goldenPath/hg17/chromosomes/. You'll find instructions for obtaining our source programs and utilities here. Some programs that you may find useful are nibFrag and twoBitToFa, as well as other fa* programs. To obtain usage information about most programs, execute it without arguments.

B. Use the Table browser to extract sequence. This is a convenient way to obtain small amounts of sequence.

1. Create a custom track of the genomic coordinates in BED format and upload into the Genome Browser.
2. Select the custom track in the Table browser, then select the "sequence" output format to retrieve data. We recommend that you save the file locally as gzip.

Question:
"How do I download data using the UCSC DAS server?"

Response:
The UCSC DAS server provides access to genome annotation data for all current assemblies featured in the Genome Browser. To view a list of the assemblies available from the DAS server and their base URLs, see http://genome.ucsc.edu/cgi-bin/das/dsn.

To construct a DAS query, combine an assembly's base URL with the sequence entry point and type specifiers available for that assembly. The entry point specifies chromosome position, and the type indicates the annotation table requested. You can view the lists of entry points and types available for an assembly with requests of the form:

	http://genome.ucsc.edu/cgi-bin/das/[db_name]/entry_points
	http://genome.ucsc.edu/cgi-bin/das/[db_name]/types

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:

	http://genome.ucsc.edu/cgi-bin/das/hg16/features?segment=1:1,100000;type=refGene

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

Response:
The Genome Browser source code and executables are freely available for academic, nonprofit, and personal use (see Licensing the Genome Browser or Blat for commerical licensing requirements). The latest version of the source code may be downloaded here.

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

Question:
"Do you have restrictions on the amount of downloads one can do?"

Response:
Generally, we'd prefer that you not hit our interactive site with programs, unless they are themselves front ends for interactive sites. We can handle the traffic from all the clicks that biologists are likely to generate, but not from programs. Program-driven use is limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day.

If you need to run batch Blat jobs, see Downloading Blat source and documentation for a copy of Blat you can run locally.

Question:
"I am trying to look at the final decoding of the human genome. How can I open the *.fa files?"

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

Unless you have a particular need to view or use the raw data files, you might find it more interesting to look at the data using the Genome Browser. Type the name of a gene in which you're interested into the position box (or use the default position), then click the submit button. In the resulting Genome Browser display, click the DNA link on the menu bar at the top of the page. Select the Extended case/color options button at the bottom of the next page. Now you can color the DNA sequence to display which portions are repeats, known genes, genetic markers, etc.

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

Response:
Yes. The Genome Browser and Table Browser are both driven by the same underlying MySQL database. Check that your downloaded tables are from the same assembly version as the one you are viewing in the Genome Browser. If the assembly dates don't match, the coordinates of the data within the tables may differ. In a very rare instance, you could also be affected by the brief lag time between the update of the live databases underlying the Genome Browser and the time it takes for text dumps of these databases to become available in the downloads directory.

Question:
"I noticed several characters other than A, C, G, T, and N in my fasta file, for example y, k, s, etc. Is the file corrupted or are these characters valid?"

Response:
The characters most commonly seen in sequence are A, C, G, T, and N, but there are several other valid characters that are used in clones to indicate ambiguity about the identity of certain bases in the sequence. It's not uncommon to see these "wobble" codes at polymorphic positions in DNA sequences. The following chart (IUPAC-IUB Symbols for Nucleotide Nomenclature: Cornish-Bowden (1985). Nucl. Acids Res. 13:3021-3030) lists nucleotide symbols, including those used for ambiguity:

          		--------------------------------------
          		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
			

Question:
"I am interested in ESTs. How do you select which ones from GenBank to display in the Genome Browser?"

Response:
All ESTs in GenBank on the date of the track data freeze for the given organism are used - none are discarded. When two ESTs have identical sequences, both are retained because this can be significant corroboration of a splice site.

ESTs are aligned against the genome using the Blat program. When a single EST aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within a selected percentage of the best are kept. Alignments must also have a minimum base identity to be kept. For more information on the selection criteria specific to each organism, consult the description page accompanying the EST track for that organism.

The maximum intron length allowed by Blat is 500,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. If an EST aligns non-contiguously (i.e. an intron has been spliced out), it is also a candidate for the Spliced EST track, provided it meets various quality controls for intron and exon length and match quality. Start and stop coordinates of each alignment block are available from the appropriate table within the Table Browser.

Note that only 250 EST tracks can be viewed at a time within the browser. If more than 250 tracks exist for the selected region, the display defaults to a denser display mode to prevent the user's web browser from being overloaded. You can restore the EST track display to a fuller display mode by zooming in on the chromosomal range or by using the EST track filter to restrict the number of tracks displayed.

For tracks such as Non[Organism] ESTs and Non[Organism] mRNAs, some selection is done on the full set at GenBank. If a sequence is too divergent from the organism's genome to generate a significant Blat hit, it is not included in the track.

Question:
"Could you help me with my interpretation of EST data? If the EST is taken from the minus (-) strand, does this always mean that the transcript is generated on the minus strand? Are two corresponding ESTs that are assigned - and + always complementary?

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

• BQ016549 (chr22:22,310,674-22,332,143 on hg18): + strand in text and - strand in graphical display
• AA928010 (chr22:20,345,264-20,354,528 on hg18): - strand in text and + strand in graphical display.

Response:
From the examples above, it can be seen that the strand to which an EST aligns is not necessarily reflected in the direction of transcription shown by the arrows in the display. When UCSC downloads mRNAs and ESTs from GenBank and aligns them to a genome assembly using Blat, each EST aligns to the + or - strand (forward or reverse direction) of the genome, which we record as + or - in the strand field of the corresponding database table, e.g. all_ests or chrN_est. The strand information (+/-) therefore indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated. Determining the direction of transcription for ESTs is not an easy task so we do some calculations to make the best guess for the transcription direction.

ESTs are sequenced from either the 5' or the 3' end. When sequenced from the 5' end, the resulting sequence is the same as that of the mRNA which it represents. With a 3' end read, the resulting sequence matches the opposite strand of the cDNA clone. Therefore, it is the reverse complement of the actual mRNA sequence. A problem occurs if the EST contributor reverse-complements the 3'-read sequence before depositing it into GenBank, with the idea that people will want the mRNA (transcription-direction) sequence. It is not always possible to determine if this has been done. Therefore, we do some calculations to try to determine the correct direction of transcription for the EST sequence.

If an EST alignment produces canonical introns (with gt-ag splice-site pairs), this is used to determine the transcription direction. For example when an EST is aligned to the genome, a canonical intron would look like this:

NNNNexonNNNNgtnnnnintronnnnnnnnagNNNNexon

Here, the two nucleotides on either end of the intron show the canonical gt-ag splice site pairs. To find transcription direction, we use a method that relies on finding gt-ag canonical pairs in one direction more often than in the opposite direction. The calculation is:

gt/ag introns minus ct/ac introns = intronOrientation

The sign of this calculated intronOrientation field (stored in the estOrientInfo table) shows the orientation of the transcript relative to the EST. Therefore, if intronOrientation is positive, then the EST appears in the display with the arrows pointing in the same direction as the EST alignment. If intronOrientation is negative, then the arrows point in the opposite direction. If no introns exist or all of the introns are non-canonical, then intronOrientation is set to zero. In both BQ016549 and AA928010 (in the example above), the intronOrientation is negative; therefore, the arrows on the Genome Browser display point in the opposite direction to that indicated by the alignment on the EST details page. Note: A low intronOrientation number can cause an incorrect assignment of transcription direction when calculated in this way.

The alignment details pages and the Table Browser do not take the intron orientation into account. They show only the alignment of the GenBank sequence (as given) to the genome. If the alignment is used to retrieve DNA sequence from the genome, the DNA sequence will look similar to the GenBank sequence (not its complement).

Question:
"Why isn't my refseq ID in your database?"

Response:
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.

Question:
"Do chrN.fa tables contain both finished and draft segments? If so, how do you determine which segments are finished?"

Response:
Yes, these tables contain both finished and draft segments. Use the corresponding chrN_gold table to look them up. The quality of the draft varies. In general, the larger the contig it is in, the better the quality. The quality of the last 500 bases on either end of a contig tends to be lower than the rest of the contig.

How do you determine the accuracy? The base-calling program Phred analyzes the traces from the sequencing machines and assigns a quality score to these. These quality scores are used by the Phrap assembly program, which gives quality scores for the bases on the assembly as well.

Question:
"What are the chrN_random_[table] files in the human assembly? Why are they called random? Is there something biologically random about the sequence in these tables or are they just not placed within their given chromosomes?"

Response:
In the past, these tables contained data related to sequence that is known to be in a particular chromosome, but could not be reliably ordered within the current sequence.

Starting with the April 2003 human assembly, these tables also include data for sequence that is not in a finished state, but whose location in the chromosome is known, in addition to the unordered sequence. Because this sequence is not quite finished, it could not be included in the main "finished" ordered and oriented section of the chromosome.

Also, in a very few cases in the April 2003 assembly, the random files contain data related to sequence for alternative haplotypes. This is present primarily in chr6, where we have included two alternative versions of the MHC region in chr6_random. There are a few clones in other chromosomes that also correspond to a different haplotype. Because the primary reference sequence can only display a single haplotype, these alternatives were included in random files. In subsequent assemblies, these regions have been moved into separate files (e.g. chr6_hla_hap1).

Question:
"What is ChrUn?"

Response:
ChrUn contains clone contigs that can't be confidently placed on a specific chromosome. For the chrN_random and chrUn_random files, we essentially just concatenate together all the contigs into short pseudo-chromosomes. The coordinates of these are fairly arbitrary, although the relative positions of the coordinates are good within a contig. You can find more information about the data organization and format on the Data Organization and Format page.

Question:
"What is chromosome M (chrM)?"

Response:
Mitochondrial DNA.

Question:
"When I download human chr22 from your web site, the unzipped file contains only N's."

Response:
There is a large block of N's at the beginning and end of chr22. Search for an A to bypass the initial group of N's.

Question:
"On the mm6 assembly, I've found duplicate contigs that are placed on both chrY and chrY_random. Is this intentional?"

Response:
On the mm6 assembly, chrY_random erroneously contains a region duplicated from chrY. Because NCBI discovered this assembly problem after the UCSC Genome Browser was processed, we were not able to remove it from mm6 prior to the browser's release. The duplicated section occupies chrY:1-696,521 and chrY_random:29,615,053-30,311,573 (the end of the chromosome) and includes the following repeated fragments:

• AC139318.5
• AC134433.3
• AC145392.2
• AC148319.2
• AC145571.3
• AC145393.4

Question:
"I have heard that the Build 32 mouse assembly isn't as good as the Build 30 assembly. Can you clarify?"

Response:
Unfortunately, there appear to be some problems with the Build 32 assembly. Ensembl has conducted an analysis of the assembly and has attributed the problems to incorrect mapping information that led to the generation of artificial duplications and some incorrect flips in orientation. You can read more information about the problems Ensembl identified and review a list of the chromosomes and genes most likely to be affected by these issues on the Ensembl Mus musculus web page.

Question:
How do the chimp and human chromosome numbering schemes compare?

Response:
The following table shows the mapping of chromosomes in the chimp draft assemblies to human chromosomes. Starting with the panTro2 assembly, the numbering scheme has been changed to reflect a new standard that preserves orthology with human chromosomes. Initially proposed by E.H. McConkey in 2004, the new numbering convention was subsequently endorsed by the International Chimpanzee Sequencing and Analysis Consortium. This standard assigns the identifiers "2a" and "2b" to the two chimp chromosomes that fused in the human genome to form chromosome 2 and renumbers the other chromosomes to more closely match their human counterparts. As a result, chromosomes 2 and 23 (present in the panTro1 assembly) do not exist in later versions.

Human Chr	Chimp Chr (panTro1)	Chimp Chr (panTro2)
1	1	1
2 (part)	12	2a
2 (part)	13	2b
3	2	3
4	3	4
5	4	5
6	5	6
7	6	7
8	7	8
9	11	9
10	8	10
11	9	11
12	10	12
13	14	13
14	15	14
15	16	15
16	18	16
17	19	17
18	17	18
19	20	19
20	21	20
21	22	21
22	23	22
X	X	X
Y	Y	Y

Question:
"I've been researching a specific area of the human genome on the current assembly, and now you've just released a new version. Is there an easy way to locate my area of interest on the new assembly?"

Response:
You can migrate data 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 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 Utilities 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 UCSC-generated over.chain file as input. Pre-generated files are 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.

Question:
"I have the accession number for a gene and would like to link it to the gene name. Is there a table that shows both pieces of information?"

Response:
If you are looking at the RefSeq Genes, the refFlat table contains both the gene name (usually a HUGO Gene Nomenclature Committee ID) and its accession number. For the Known Genes, use the kgAlias table.

Question:
"How can I obtain a complete list of all the genes in the UCSC Known Genes table for a particular organism?

Response:
To obtain a complete copy of the entire Known Genes data set for an organism, open the Genome Browser Downloads page, jump to the section specific to the organism, click the Annotation database link in that section, then click the link for the knownGene.txt.gz table.

Data for a specific region or chromosome may be obtained from the Table Browser by selecting the "Genes and Gene Prediction Tracks" group, the "Known Genes" track and the "knownGene" table. Set the position to the region of interest, then click the "get output" button.

Question:
"What version of RepeatMasker do you use on your data? Which flags do you use?"

Response:
UCSC uses the latest versions of RepeatMasker and repeat libraries available on the date when the assembly data is processed. RepeatMasker version information can usually be found in the README text for the assembly's bigZips downloads directory.

Masking is done using the RepeatMasker -s flag. For mouse repeats, we also use -m. In addition to RepeatMasker, we use the Tandem Repeat Finder (trf) program, masking out repeats of period 12 or less. The repeats are just "soft" masked. Alignments are allowed to extend through repeats, but not initiate in them.

Question:
"Are the repeat annotation files available for every chromosome?"

Response:
Yes, you can obtain the repeat-masked files via the Table Browser or from the organism's annotation database downloads directory. The RepeatMasker annotation tables are named chrN_rmsk (where N represents the chromosome number) and the Tandem Repeat Finder (TRF) tables are named simpleRepeat.

Question:
"When I run RepeatMasker independently from the RepeatMasker web server, my results vary from those of UCSC. What's the cause?"

Response:
UCSC occasionally uses updated versions of the RepeatMasker software and repeat libraries that are not yet available on the RepeatMasker website (see Repeat-masking data for more information).

Question:
"How can I fetch promoter sequence upstream of a gene?"

Response:
The UCSC Genome Browser offers several ways to obtain this information, depending on your requirements.

The Genome Browser downloads site provides prepackaged downloads of 1000 bp, 2000 bp, and 5000 bp upstream sequence for RefSeq genes that have annotated 5' UTRs. You can obtain these from the bigZips downloads directory for the assembly of interest.

To fetch the upstream sequence for a specific gene, use the Table Browser. Enter the genome, assembly, and select the knownGene table. Paste the gene name or accession number in the identifier field. Choose sequence for the output format type, then click the get output button. On the next page, select genomic. On the final page, you will have the opportunity to configure the amount of upstream promoter sequence to fetch, along with several other options. Click Get Sequence when you've finished configuring the output.

You can also use the Genome Browser to obtain sequence for a specific gene. Open the Genome Browser window to display the gene in which you're interested. Click the entry for the gene in the RefSeq or Known Genes track, then click the Genomic Sequence link. Alternatively, you can click the DNA link in the top menu bar of the Genome Browser tracks window to access options for displaying the sequence.

The Stanford Human Promoters track on the UCSC Custom Annotation Tracks page shows promoters for some of the human assemblies.

Question:
"Where can I download the conservation score data from the Human/Mouse Evolutionary Conservation Score track?"

Response:
The conservation score data are stored in a group of tables in the annotation database downloads directory. The naming conventions of the tables vary among releases. In earlier assemblies, table names are of the form chrN_humMusL, chrN_zoom1_humMusL, and or chrN_zoom2500_humMusL. In later releases, the tables are named using specific release numbers, such as chrN_hg16Mm3. The tables within a given set differ by the number of bases/score interval and are used to generate the browser displays at different zooming levels.

Question:
"I downloaded the axtNet alignments between the latest human and mouse assemblies. I found that some of the alignments listed in the axtNet files do not agree with what is shown in the browser."

Response:
Is this alignment on the minus strand? Minus strand coordinates in axt files are handled differently from how they are handled in the Genome Browser. To convert axt minus strand coordinates to Genome Browser coordinates, use:

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

Question:
"How do I map the STS genetic marker IDs in the genome browser to the IDs assigned by other groups? "

Response:
We assign our own IDs to each of the STS markers, but we also track the UniSTS IDs for each marker in the downloadable stsInfo2 table. To determine the location of a specific marker, look up the marker's name in the stsAlias table to determine the UCSC ID assigned to the marker, and then use this ID to look it up in the stsMap table where the marker is located. For example, D10S249 has UCSC ID 2880 and is located at chr10:240791-241019.

Question:
"Where can I get more information about the deCODE map?"

Response:
You can obtain this information from the combination of a couple of tables. The stsMap table contains the physical position of all STS markers, including those on the deCODE map. This file also contains information about the position on the genome-wide maps, including the deCODE map. A second file, stsInfo2, contains additional information about each marker, including aliases, primer sequence information, etc. This table is related to the first table by an ID (the identNo field in both files).

Question:
"Is it possible to run SQL queries directly on the database rather than using the Table Browser interface?"

Response:
In response to requests from Genome Browser users, we have set up a MySQL database for public access at genome-mysql.cse.ucsc.edu. This new server allows MySQL access to the same set of data currently available on our public Genome Browser site. The data are synchronized weekly with the main databases on http://genome.ucsc.edu. During this synchronization period, the MySQL server can be intermittently out of sync with the main website for a short period. The weekly synchronization takes place on Monday mornings from 4:00 am to 9:00 am Pacific Time.

To connect to the database, you must use a computer on which the MySQL client libraries have been installed. We recommend you use the most current version of v5.0 MySQL clients, which may be downloaded from http://dev.mysql.com/downloads/mysql/5.0.html. Connect to the MySql server using the command:

    mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A

Once connected to the database, you may use a wide range of MySQL commands to query the database. As a courtesy to others, please observe the following guidelines when using the database:

• Avoid excessive or heavy queries that may impact the server performance. Inappropriate query use will result in a restriction of access. If you plan to execute a query that you think may be excessive, contact UCSC first to avoid the possibility of having your access blocked.
• Bot access and excessive program-driven use are not permitted.
• Attachments by local mirror sites are prohibited.

The MySQL database can also be used by the numerous utilities in the kent source tree. Add the following specifications to your $HOME/.hg.conf file (remember to chmod your .hg.conf file to 600 permissions):

    db.host=genome-mysql.cse.ucsc.edu
    db.user=genomep
    db.password=password 

If you prefer a more structured graphical interface to the UCSC database tables, use the Table Browser.

System problems should be reported to genome-www@soe.ucsc.edu. Send questions regarding the database contents or queries to genome@soe.ucsc.edu. Messages sent to this address will be posted to the moderated genome mailing list, which is archived on a public Web-accessible pipermail archive. This archive may be indexed by non-UCSC sites such as Google.