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The bigPsl format stores alignments between two sequences, as
PSL files do, but they are compressed and indexed as
bigBeds. bigPsl files are created using the program
bedToBigBed with a special AutoSQL
file that defines the fields of the bigPsl. The resulting bigPsl files are in an indexed binary
format. The main advantage of the bigPsl files is that only portions of the files needed to display
a particular region are transferred to UCSC. So for large data sets, bigPsl is considerably faster
than regular PSL files. The bigPsl file remains on your web accessible server (http, https, or
ftp), not on the UCSC server. Only the portion that is needed for the chromosomal position you are
currently viewing is locally cached as a "sparse file".
The following AutoSQL definition is used for bigPsl gene prediction files. This is the
bigPsl.as file defined by the
table bigPsl "bigPsl pairwise alignment" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name or ID of item, ideally both human readable and unique" uint score; "Score (0-1000)" char strand; "+ or - indicates whether the query aligns to the + or - strand on the reference" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "RGB value (use R,G,B string in input file)" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" uint oChromStart;"Start position in other chromosome" uint oChromEnd; "End position in other chromosome" char oStrand; "+ or -, - means that psl was reversed into BED-compatible coordinates" uint oChromSize; "Size of other chromosome." int[blockCount] oChromStarts; "Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand" lstring oSequence; "Sequence on other chrom (or empty)" string oCDS; "CDS in NCBI format" uint chromSize;"Size of target chromosome" uint match; "Number of bases matched." uint misMatch; " Number of bases that don't match " uint repMatch; " Number of bases that match but are part of repeats " uint nCount; " Number of 'N' bases " uint seqType; " 0=empty, 1=nucleotide, 2=amino_acid" )
Note that the oStrand field is an indicator of whether or not the stored psl needs to be reverse complemented before output or display. This is due to the need for the bigPsl file to have reference coordinates on the positive strand which is a requirement of the BED format. The strand field indicates whether the positions in oChromStarts are listed from the beginning (+) or the end of the chromosome (-).
Note that the
bedToBigBed utility uses a substantial amount of memory; somewhere on the
order of 1.25 times more RAM than the uncompressed BED input file.
To create a bigPsl track, follow these steps:
pslToBigPslprograms from the directory of binary utilities.
fetchChromSizesscript from the same directory to create a chrom.sizes file for the UCSC database you are working with (e.g., hg38). Alternatively, you can download the chrom.sizes file for any assembly hosted at UCSC from our downloads page (click on "Full data set" for any assembly). For example, for the hg38 database, the hg38.chrom.sizes are located at http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
bed12+13bigPsl format file that has the 25 fields described by a bigPsl file as described here.
oChromStart, oChromEnd, oStrand, oChromSize, oChromStarts, oSequence, oCDS, chromSize, match, misMatch, repMatch, nCount, seqType
pslToBigPslutility to create a correctly formatted
bed12+13file like so:
pslToBigPsl bigPsl.psl stdout | sort -k1,1 -k2,2n > bigPsl.txt
pslToBigPslto generate a more informative final bigPsl file:
pslToBigPsl bigPsl.psl -cds=bigPsl.cds -fa=bigPsl.fa stdout | sort -k1,1 -k2,2n > bigPsl.txt
bedToBigBedutility like so:
bedToBigBed -as=bigPsl.as -type=bed12+13 -tab bigPsl.txt chrom.sizes bigPsl.bb
bigPsl.bb) to an http, https, or ftp location.
track type=bigPsl name="My Big Psl" description="Some mRNAs Discovered from Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigPsl.bb
bedToBigBed program can also be run with several additional options. Run
bedToBigBed with no arguments to view a full list of the available options.
In this example, you will use an existing bigPsl file to create a bigPsl custom track. A bigPsl file that contains data on the hg38 assembly has been placed on our http server. You can create a custom track using this bigPsl file by constructing a "track" line that references this file like so:
track type=bigPsl name="bigPsl Example One" description="A bigPsl file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigPsl.bb
Paste the above "track" line into the custom track management page for the human assembly hg38, then press the "submit" button.
Custom tracks can also be loaded via one URL line. The below link loads the same bigPsl track, but includes parameters on the URL line:
With this example bigPsl loaded, click into an item from the track. Note how the details page displays information about the alignment, similar to PSL tracks, as well as links to display the browser position of the alignment and more detailed information about the alignment.
In this example, you will create your own bigPsl file from an existing bigPsl input file.
bed12+13bigPsl.txt example input file to your machine (satisfies above step 4).
bedToBigBedutility (step 2).
hg38.chrom.sizestext file to your machine. It contains the chrom.sizes for the human (hg38) assembly (step 3).
bigPsl.astext file to your machine.
bedToBigBed -as=bigPsl.as -type=bed12+13 -tab bigPsl.txt hg38.chrom.sizes bigPsl.bb
bigPsl.bb) on a web-accessible server (step 6).
If you would like to share your bigPsl data track with a colleague, learn how to create a URL by looking at Example 11 on this page.
Since the bigPsl files are an extension of bigBed files, which are indexed binary files, they can be difficult to extract data from. We have developed the following programs, all of which are available from the directory of binary utilities.
bigBedToBed— this program converts a bigBed file to ASCII BED format.
bigBedSummary— this program extracts summary information from a bigBed file.
bigBedInfo— this program prints out information about a bigBed file.
As with all UCSC Genome Browser programs, simply type the program name at the command line with no parameters to see the usage statement.
If you encounter an error when you run the
bedToBigBed program, it may be because your
input bigPsl file has data off the end of a chromosome. In this case, use the
program here before the
bedToBigBed program. It will remove the row(s) in your input BED file that are off the
end of a chromosome.