bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigPsl.html src/hg/htdocs/goldenPath/help/bigPsl.html index 2fbcabf0a89..a62e747ccc4 100755 --- src/hg/htdocs/goldenPath/help/bigPsl.html +++ src/hg/htdocs/goldenPath/help/bigPsl.html @@ -93,42 +93,42 @@

Creating a bigPsl track

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.

Step 2. Download the bedToBigBed and pslToBigPsl programs from the -binary utilities directory.

+binary utilities directory.

Step 3. Use the fetchChromSizes script from the -same directory to create a +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 +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 -http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.

+http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.

Step 4. Use the 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: oChromStart, oChromEnd, oStrand, oChromSize, oChromStarts, oSequence, oCDS, chromSize, match, misMatch, repMatch, nCount, and seqType.

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 bigPsl file:

pslToBigPsl bigPsl.psl -cds=bigPsl.cds -fa=bigPsl.fa stdout | sort -k1,1 -k2,2n > bigPsl.txt

@@ -183,68 +183,68 @@

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.

Example #2

In this example, you will create your own bigPsl file from an existing bigPsl input file.

Save the example bed12+13 file bigPsl.txt to your computer (Step 4 in Creating a bigPsl track, above).
Download the - bedToBigBed utility + bedToBigBed utility (Step 2, above).
Save the hg38.chrom.sizes text file to your computer. This file contains the chrom.sizes for the human (hg38) assembly (Step 3, above).
Save the autoSql file bigPsl.as to your computer.

Run the bedToBigBed utility to create the bigPsl output file (Step 5, above):

bedToBigBed -as=bigPsl.as -type=bed12+13 -tab  bigPsl.txt hg38.chrom.sizes bigPsl.bb

Place the newly created bigPsl file (bigPsl.bb) on a web-accessible server (Step 6, above).
Construct a track line that points to the bigPsl file (Step 7, above).
Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (Step 8, above).

Sharing your data with others

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.

Extracting data from the bigPsl format

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.

+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.

Troubleshooting

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 the bedClip program -(available here) to remove the problematic +(available here) to remove the problematic row(s) in your input file before running the bedToBigBed program.