fe2053eb5d1611d03b4c4f91e53aba4ac6e0178a braney Sat Sep 12 15:29:42 2020 -0700 placeholders for bigLolly help diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index 720cb5f..2536ea2 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -13,30 +13,31 @@ <!-- Left column --> <div class="col-md-6"> <ul> <li><a href="../goldenPath/help/axt.html">Axt format</a></li> <li><a href="#format5.1">BAM format</a></li> <li><a href="#format1">BED format</a></li> <li><a href="#format1.7">BED detail format</a></li> <li><a href="#format1.8">bedGraph format</a></li> <li><a href="#format21">barChart and bigBarChart format</a></li> <li><a href="#format1.5">bigBed format</a></li> <li><a href="#format9.1">bigGenePred table format</a></li> <li><a href="#format9.2">bigPsl table format</a></li> <li><a href="#format9.3">bigMaf table format</a></li> <li><a href="#format9.4">bigChain table format</a></li> <li><a href="#format9.5">bigNarrowPeak table format</a></li> + <li><a href="#format9.6">bigLolly table format</a></li> <li><a href="#format6.1">bigWig format</a></li> <li><a href="../goldenPath/help/chain.html">Chain format</a></li> </ul> </div> <!-- Right column --> <div class="col-md-6"> <ul> <li><a href="#format5.2">CRAM format</a></li> <li><a href="#format9">GenePred table format</a></li> <li><a href="#format3">GFF format</a></li> <li><a href="#format4">GTF format</a></li> <li><a href="#format20">HAL format</a></li> <li><a href="#format23">Hic format</a></li> <li><a href="#format22">Interact and bigInteract format</a></li> <li><a href="#format5">MAF format</a></li> @@ -1179,30 +1180,38 @@ Click <a href="../goldenPath/help/bigChain.html">here</a> for more information on the bigChain format.</p> <a name="format9.5"></a> <h2>bigNarrowPeak format</h2> <p> bigNarrowPeak is a format used to provide called peaks of signal enrichment based on pooled, normalized (interpreted) data. It is a BED6+4 format. bigNarrowPeak format is equivalent to the <a href="FAQformat.html#format12">narrowPeak</a> text-based format supported using the <a href="FAQformat.html#format1.5">bigBed</a> format, so it can be efficiently accessed over a network.</p> <p> Click <a href="../goldenPath/help/bigNarrowPeak.html">here</a> for more information on the bigNarrowPeak format.</p> +<a name="format9.6"></a> +<h2>bigLolly format</h2> +<p> +bigLolly is a format used to draw a lollipop chart. It's a standard bigBed format where the score is used to decide how high to draw the lollipop. There are trackDb options to specify which fields to use for the height and width of the lollipop. +<p> +Click <a href="../goldenPath/help/bigLolly.html">here</a> for more information on the bigLolly +format.</p> + <a name="format10"></a> <h2>Personal Genome SNP format</h2> <p> This format is for displaying SNPs from personal genomes. It is the same as is used for the Genome Variants and Population Variants tracks.</p> <ol> <li> <strong>chrom</strong> - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).</li> <li> <strong>chromStart</strong> - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.</li> <li> <strong>chromEnd</strong> - The ending position of the feature in the chromosome or scaffold. The <em>chromEnd</em> base is not included in the display of the feature. For example, the first 100