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. ChrUn contains clone contigs that cannot be confidently placed on a specific chromosome.
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. There is a large block of N s at the beginning and end of chr Search for an A to bypass the initial group of N s.
The following table shows the mapping of chromosomes in the chimp draft assemblies to human chromosomes. Starting with the panTro2 assembly, the numbering scheme was changed to reflect a new standard that preserves orthology with human chromosomes. Initially proposed by E.
McConkey in , 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. 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. 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.
For the Known Genes, use the kgAlias table. 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. Set the position to the region of interest, then click the "get output" button. UCSC uses the latest versions of RepeatMasker and repeat libraries available on the date when the assembly data is processed.
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. Yes, you can obtain the repeat-masked files via the Table Browser or from the organism's annotation database downloads directory.
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. The Genome Browser downloads site provides prepackaged downloads of bp, bp, and bp upstream sequence for RefSeq genes that have a coding portion and annotated 5' and 3' 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. 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 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.
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:. See an explanation of coordinate transforms in the genomeWiki. 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.
You can obtain this information from the combination of a couple of tables. 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. The fourth column of the BED output contains a lot of information separated by underscores.
For example:. The raw data underlying a track can be explored interactively with the Table Browser , Data Integrator , or Variant Annotation Integrator. 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. One final note: If you are interested in downloading only a small portion of the track for example, just a region on chromosome 8 , you can download this region using the UCSC Table browser.
Here's how to do this: 1 Follow steps 1 and 2 above. This will take you to the UCSC Table Browser where all the fields will already be filled in with the track you are interested in. Select get output and your file will be downloaded.
There is no need to unzip unless you chose the gzip compressed option. Best wishes and good luck analyzing UCSC data tracks! Email This BlogThis! Transcription Factor Binding Sites. FSU Repli-chip. HAIB Genotype. Stanf Nucleosome. UW Repli-seq. Duke Affy Exon. Open Chromatin. HAIB Methyl-seq.
Gencode Genes. Enhancer H3K27Ac. Enhancer H3K4Me1. Promoter H3K4Me3. Helicos RNA-seq. HudsonAlpha RNA-seq. Yale RNA-seq.
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