687a9c88647a46f71d40f2d04b77251b5a9cff55 max Fri May 31 08:06:39 2024 -0700 section docs, refs #17950 diff --git src/hg/htdocs/goldenPath/help/bigPsl.html src/hg/htdocs/goldenPath/help/bigPsl.html index 9a470f4..3761f45 100755 --- src/hg/htdocs/goldenPath/help/bigPsl.html +++ src/hg/htdocs/goldenPath/help/bigPsl.html @@ -60,31 +60,31 @@ 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>Since bigPsl is just a bigBed file, in addition to these fields, bigPsl +<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> 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>