ac67c40af43801ce6a8bb6e7fe1beeb2b49fb355 gperez2 Mon Jun 3 04:50:49 2024 -0700 Adding a additional fields note for the bigPsl Track Format page, refs #17950 diff --git src/hg/htdocs/goldenPath/help/bigPsl.html src/hg/htdocs/goldenPath/help/bigPsl.html index 3761f45..2fbcabf 100755 --- src/hg/htdocs/goldenPath/help/bigPsl.html +++ src/hg/htdocs/goldenPath/help/bigPsl.html @@ -60,38 +60,43 @@ 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" ) </code></pre> <p> The value of the <code>oStrand</code> 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 <code>strand</code> field indicates whether the positions in <code>oChromStarts</code> are listed from the chromosome beginning (+) or end (-).</p> -<p><b>Addtional extra fields:</b> Since bigPsl is just a bigBed file, in addition to these fields, bigPsl -files can have any number of additional, extra bigBed fields, as -long as they are defined after the seqType field. -See <a href="bigBed.html#Ex3">Example 3</a> of the bigBed documentation page for -sample .as and .bed files. These fields can also be used for custom <a -href="https://genome-blog.gi.ucsc.edu/blog/2022/06/28/track-hub-settings/">mouseOvers</a>, -feature filters and coloring options. Contact us if you run into difficulty -using them.</p> +<p><b>Additional fields:</b> +Since a bigPsl file is a bigBed file, additional fields can be added as bigBed fields. The +additional bigBed fields are defined after the seqType field of the bigPsl.as file. +See <a href="bigBed.html#Ex3">Example 3</a> of the bigBed Track Format page for an example +on how to create a bigBed file with extra (custom) fields. The additional fields can be used for +custom +<a href="https://genome-blog.gi.ucsc.edu/blog/2022/06/28/track-hub-settings/">mouseOvers</a>, +feature filters, and coloring options. Contact us at +<A HREF="mailto:genome-www@soe. +ucsc. +edu"> +genome-www@soe.ucsc.edu +</A> if you run into difficulty using them.</p> <p> The <code>bedToBigBed</code> utility uses a substantial amount of memory: approximately 25% more RAM than the uncompressed BED input file. The -maxAllow option to bedToBigBed can be used to allow the tool to use more than 16GB of RAM.</p> <h2>Creating a bigPsl track</h2> <p> To create a bigPsl track, follow these steps:</p> <p> <strong>Step 1.</strong> If you already have a PSL file created using BLAT or another tool, skip to <em>Step 2</em>. Otherwise, download the example PSL file <a href="examples/bigPsl.psl"><em>bigPsl.psl</em></a> for the human GRCh38/hg38 assembly. You will also want to download the files <a href="examples/bigPsl.fa"><em>bigPsl.fa</em></a> and