8e2ce67692e814db90b2d2938915712ff9b0ee51 jeltje.van.baren Wed Apr 16 18:07:03 2025 -0700 Adding recount3 #34886 diff --git src/hg/makeDb/trackDb/recount3.html src/hg/makeDb/trackDb/recount3.html new file mode 100644 index 00000000000..1dfccbf8870 --- /dev/null +++ src/hg/makeDb/trackDb/recount3.html @@ -0,0 +1,81 @@ +<!DOCTYPE html> +<html> +<head> +</head> + +<body> +<h2>Description</h2> +<p> +Recount3 is a comprehensive resource for re-analyzing RNA-seq data. It provides uniformly processed +RNA-seq data and associated metadata from a wide range of studies, enabling researchers to access +and analyze gene expression data in a consistent manner. Recount3 aggregates data from multiple +sources, including the Sequence Read Archive (SRA) and the Genotype-Tissue Expression (GTEx) project, +and reprocesses it using a standardized pipeline. This allows for cross-study comparisons and +meta-analyses, facilitating discoveries in genomics and transcriptomics. +</p><p> +These tracks display the recount3 intron data including split read counts. +</p> + + +<h2>Display Conventions</h2> +<p> +Intron blocks are grayscale colored based on read support (darker tones indicate higher coverage). <br> +Split read counts and splice motifs are shown on mouseover. <br> +By default only introns with a minimum read count of 10,000 are shown. This setting can be changed +on the track configuration page. <br> +The intron ends are color coded: +<ul> +<li><b><font color="#2E2585">Dark blue</font></b> GT donors and AG acceptors (CT and AC on +the minus strand) </li> +<li><b><font color="#5DA899">Teal</font></b> GC donors (GT on the minus strand) </li> +<li><b><font color="#C26A77">Faded red</font></b> AT donors and AC acceptors (GT and GT on the +minus strand) </li> +</ul> +Introns with non standard ends do not have colored tags. +<br> +The SRA track is only visible when zoomed in within 10 million bases because of its data density. +</p> + +<h2>Data Access</h2> +The raw data can be explored interactively with the +<a href="https://genome.ucsc.edu/cgi-bin/hgTables">Table Browser</a> or the +<a href="https://genome.ucsc.edu/cgi-bin/hgIntegrator">Data Integrator</a>. +For automated analysis, the data may be queried from our +<a href="https://genome.ucsc.edu/goldenPath/help/api.html">REST API</a>.<br> +Please refer to our +<a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing list archives</a> +for questions, or our +<a href="https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloads36">Data Access FAQ</a> +for more information. +<p> +The original junction files can be found at <br> +<a href="https://snaptron.cs.jhu.edu/data/gtexv2/junctions.tgz" target="_blank"> +https://snaptron.cs.jhu.edu/data/gtexv2/junctions.tgz</a><br> +<a href="https://snaptron.cs.jhu.edu/data/tcgav2/junctions.tgz" target="_blank"> +https://snaptron.cs.jhu.edu/data/tcgav2/junctions.tgz</a><br> +<a href="https://snaptron.cs.jhu.edu/data/srav3h/junctions.tgz" target="_blank"> +https://snaptron.cs.jhu.edu/data/srav3h/junctions.tgz</a><br> +<a href="https://snaptron.cs.jhu.edu/data/ccle/junctions.tgz" target="_blank"> +https://snaptron.cs.jhu.edu/data/ccle/junctions.tgz</a><br> +<a href="https://snaptron.cs.jhu.edu/data/srav1m/junctions.tgz" target="_blank"> +https://snaptron.cs.jhu.edu/data/srav1m/junctions.tgz (mouse)</a><br> +</p> + +<h2>Methods</h2> +<p> +Junction files were converted to bed format. For grayscaling total read count was log10 +transformed and multiplied by 10 to get a score between 0 and 225, which can be found +in the bed score field. +</p> + +<h2>References</h2> +<p> +Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT +<em>et al</em>. +<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02533-6" +target="_blank"> +recount3: summaries and queries for large-scale RNA-seq expression and splicing</a>. +<em>Genome Biol</em>. 2021 Nov 29;22(1):323. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34844637" target="_blank">34844637</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8628444/" target="_blank">PMC8628444</a> +</p>