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The bigPsl format stores alignments between two sequences just as
PSL files do; however, bigPsl files are compressed
and indexed as bigBeds. PSL files are converted to bigPsl
files using the program
bedToBigBed, run with the
-as option to pull in a
(.as) file that defines the fields of the bigPsl.
The bigPsl files are in an indexed binary format. The main advantage of this format is that only those portions of the file needed to display a particular region are transferred to the Genome Browser server. Because of this, bigPsl files have considerably faster display performance than regular PSL files when working with large data sets. The bigPsl file remains on your local web-accessible server (http, https or ftp), not on the UCSC server, and only the portion needed for the currently displayed chromosomal position is locally cached as a "sparse file". If you do not have access to a web-accessible server and need hosting space for your bigPsl files, please see the Hosting section of the Track Hub Help documentation.
The following autoSql definition is used to specify bigPsl alignment files. This
definition, contained in the file bigPsl.as, is pulled in
bedToBigBed utility is run with 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" )
The value of the
oStrand field indicates whether or not the stored psl data should be
reverse-complemented before it is outputted or displayed. This is necessary because the bigPsl file
stores reference coordinates on the positive strand, as required by the BED format. The
strand field indicates whether the positions in
oChromStarts are listed
from the chromosome beginning (+) or end (-).
Note that the
bedToBigBed utility uses a substantial amount of memory: approximately
25% more RAM than the uncompressed BED input file.
To create a bigPsl track, follow these steps:
Step 1. If you already have a PSL file created using BLAT or another tool, skip to Step 2. Otherwise, download the example PSL file bigPsl.psl for the human GRCh38/hg38 assembly. You will also want to download the files bigPsl.fa and bigPsl.cds if you would like to use the alternate options described in Step 4, below.
pslToBigPsl programs from the
binary utilities directory.
fetchChromSizes script from the
same directory to create a
chrom.sizes file for the UCSC database with which you are working (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, the hg38.chrom.sizes file for the hg38
database is located at
pslToBigPsl utility to create a bigPsl file in bed12+13 format that contains
the 25 fields described in the bigPsl format definition above. The file must
include the 13 extra fields:
pslToBigPsl bigPsl.psl stdout | sort -k1,1 -k2,2n > bigPsl.txt
If you are using your own PSL file, you may have corresponding FASTA and CDS files that accompany
it. You can provide these files as input to
pslToBigPsl to generate a more informative
pslToBigPsl bigPsl.psl -cds=bigPsl.cds -fa=bigPsl.fa stdout | sort -k1,1 -k2,2n > bigPsl.txt
Create the binary indexed bigPsl file from your sorted bigPsl input file using the
bedToBigBed -as=bigPsl.as -type=bed12+13 -tab bigPsl.txt chrom.sizes bigPsl.bb
Step 6. Move the newly created bigPsl file (bigPsl.bb) to a web-accessible http, https, or ftp location.
Step 7. Construct a custom track using a single track line. Note that any of the track attributes listed here are applicable to tracks of type bigBed. The most basic version of the track line will look something like this:
track type=bigPsl name="My Big Psl" description="Some mRNAs Discovered from Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigPsl.bb
Step 8. Paste the custom track line into the text box on the custom track management page.
bedToBigBed program can be run with several additional options. For a full list of
the available options, type
bedToBigBed (with no arguments) on the command line to
display the usage message.
In this example, you will create a bigPsl custom track using an existing bigPsl file, bigPsl.bb, located on the UCSC Genome Browser http server. This file contains data for the hg38 assembly.
To create a custom track using this bigPsl file:
track type=bigPsl name="bigPsl Example One" description="A bigPsl file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigPsl.bb
Custom tracks can also be loaded via one URL line. The link below loads the same bigPsl track, and sets additional display parameters in the URL:
After this example bigPsl is loaded in the Genome Browser, click on a track item in the Genome Browser's track display. Note that the details page displays information about the alignment, similar that which is available for PSL tracks, as well as links that display the browser position of the alignment and other detailed information about the alignment.
In this example, you will create your own bigPsl file from an existing bigPsl input file.
bedToBigBedutility (Step 2, above).
bedToBigBedutility to create the bigPsl output file (Step 5, above):
bedToBigBed -as=bigPsl.as -type=bed12+13 -tab bigPsl.txt hg38.chrom.sizes bigPsl.bb
If you would like to share your bigPsl data track with a colleague, learn how to create a URL by looking at Example #6 on this page.
Because bigPsl files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the binary utilities directory.
bigBedToBed— converts a bigBed file to ASCII BED format.
bigBedSummary— extracts summary information from a bigBed file.
bigBedInfo— prints out information about a bigBed file.
As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the command line to view the usage statement.
If you encounter an error when you run the
bedToBigBed program, check your input
file for data coordinates that extend past the the end of the chromosome. If these are present, run
(available here) to remove the problematic
row(s) in your input file before running the