a050a5d26e8cd5a70055da0e080980fa3bf45824 brianlee Thu Jun 2 07:31:09 2022 -0700 Adding a link in the genePred FAQ to advertise bigGenePred and codon number/AA display in custom tracks refs #26086 diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index 5bb671f..e886479 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -960,31 +960,35 @@ 1 - C 2 - A 3 - G 4 - N (unknown)</code></pre> <p> The most significant bit in a nibble is set if the base is masked. </p> <a name="format9"></a> <h2>GenePred table format</h2> <p> genePred is a table format commonly used for gene prediction tracks in the Genome Browser. Variations of the genePred format are listed below.</p> <p> If you would like to obtain browser data in GFF (GTF) format, please refer to <a href="http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format" -target="_blank">Genes in gtf or gff format</a> on the Wiki.</p> +target="_blank">Genes in gtf or gff format</a> on the Wiki. There is also a +format of genePred called <a href="../goldenPath/help/bigGenePred.html" +target="_blank">bigGenePred</a>, a version of <a href="../goldenPath/help/bigBed.html" +target="_blank">bigBed</a>, which enables custom tracks to display of codon numbers +and amino acids when zoomed in to the base level.</p> <a name=GenePredictions></a> <p><strong>Gene Predictions</strong></p> <p> The following definition is used for gene prediction tables.In alternative-splicing situations, each transcript has a row in this table.</p> <pre><code>table genePred "A gene prediction." ( string name; "Name of gene" string chrom; "Chromosome name" char[1] strand; "+ or - for strand" uint txStart; "Transcription start position" uint txEnd; "Transcription end position" uint cdsStart; "Coding region start"