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welcome.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
</head>
<body style="margin: 0">
<div class="jumbotron">
<div class="container">
<table><tr><td>
<h2>Hello, your <strong>HiCExplorer</strong> is running!</h2>
<br>
<a target="_blank" href="https://wiki.galaxyproject.org/Admin/Config" class="btn btn-primary btn-lg">Configuring Galaxy »</a>
<a target="_blank" href="https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial" class="btn btn-primary btn-lg">Installing Tools »</a>
<a target="_parent" href="/tours/hicexplorer" class="btn btn-primary btn-lg">Guided Tour »</a>
</td><td>
<div align=center>
<img src="./welcome_image.png" width="90%" height="90%" />
</div>
</td></tr>
</table>
</div>
</div>
<div class="container">
<p class="lead">
<h2> Get started with Galaxy HiCExplorer </h2>
Are you new to Galaxy, or returning after a long time, and looking for help to get started?
Take <a target="_parent" href="tours/core.galaxy_ui">a guided tour</a> through Galaxy's user interface.
Take <a target="_parent" href="/tours/hixexplorer">a guided tour</a> for an introduction to Galaxy HiCExplorer and Hi-C data analysis. This tour is guides you through the Hi-C tutorial on the <a target="_parent" href="http://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/hicexplorer/tutorial.html">Galaxy Training Network</a> where you can analyse Hi-C data of Drosophila melanogaster. Follow the tutorial to understand the analysis steps better or as a help which parameters are useful.
A precomputed history of the tutorial can be viewed online at
<a target="_parent" href="https://hicexplorer.usegalaxy.eu/u/joachim-wolff/h/drosophila-melanogaster-hi-c-training">https://hicexplorer.usegalaxy.eu</a>.
We recommend to follow the tutorial on
<a target="_parent" href="http://galaxyproject.github.io/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html">FASTQC</a> for quality checks.
<h3> Example data</h3>
The Galaxy Training Network tutorial uses Hi-C data from Drosophila melanogaster and is hosted on zenodo:
<a target="_parent" href="https://doi.org/10.5281/zenodo.1183661"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.1183661.svg" alt="DOI"></a>
<h2> Galaxy HiCExplorer -- many possibilities </h2>
<img src="./welcome_publication_plots.png" width="90%" height="90%" /><br>
<b>(A)</b> Galaxy HiCExplorer workflows and tools. Quality control tools:
<b>(B)</b> Output of hicCorrelate comparing two wild types and one knockdown samples.
<b>(C)</b> Output of hicPlotDistVsCounts that shows changes of the number of contacts for different conditions. Analysis tools:
<b>(D)</b> hicPlotMatrix of the Pearson correlation matrix derived from a contact matrix for chromosome 6 in mouse computed with hicTransform.
The optional data track at the bottom shows the first eigenvector for A/B compartment obtained using hicPCA.
<b>(E)</b> The pixel difference between a Hi-C corrected matrix for wild type condition and a knock down was computed using hicCompareMatrices
and a 7Mb region is visualized using hicPlotMatrix. Visualization tools: <b>(F)</b> Contact matrix plot of a 80 to 105 Mb region of chromosome 2 in log scale.
<b>(G)</b> Example output of hicPlotViewpoint showing the corrected number of Hi-C contacts for a single bin in chromosome 5 (output similar to 4C-seq)
(<a target="_parent" href="https://doi.org/10.1101/gr.213066.116">Andrey 2017</a>). <b>(H)</b> A Hi-C matrix was converted into an observed
vs. expected matrix using hicTransform and this matrix, together with the location of high-affinity sites from
(<a target="_parent" href="https://doi.org/10.1016/j.molcel.2015.08.024">Ramirez 2015</a>) were used to run hicAggregateContacts.
<b>(I)</b> 85 Mb to 110 Mb region from human chromosome 2 visualized using hicPlotTADs. TADs were computed by hicFindTADs.
The additional tracks added correspond to: TAD- separation score (as reported by hicFindTADs), chromatin state , principal component 1 (A/B compartment)
computed using hicPCA, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. Hi-C data for <b>B</b>, <b>C</b>, <b>E</b> and <b>H</b>
from Drosophila melanogaster S2 cells from (<a target="_parent" href="https://doi.org/10.1038/s41467-017-02525-w">Ramirez 2018</a>).
Hi-C data for <b>D</b>, <b>F</b> and <b>I</b> from mouse cardiac myocytes(<a target="_parent" href="https://doi.org/10.1038/s41467-017-01724-9 ">Nothjunge 2017</a>).
Additional tracks in <b>I</b> from (<a target="_parent" href="https://doi.org/10.1038/s41467-017-01724-9 ">Nothjunge 2017</a>).
<h2> Workflows </h2>
To automatize different consecutive steps we provide the following workflows in three categories: From scratch (FASTQ files), from scratch (FASTQ files) and summing
up replicates and if you have already your contact matrix. Many workflows require collections of FASTQ files as an input, it is shown
<a href="https://galaxyproject.org/tutorials/collections/">here</a> how to create a collection. Please do not forget to check the quality of the FASTQ files with FastQC.
Please have in mind that all workflows need additional input from the user.
All mapping steps are done with BWA-MEM and the correct reference genome need to be defined by the user.
The correct restriction site and the bin size for hicBuildMatrix needs to be defined too.
The correction of the matrix is done with the default parameters of -1.5 and 5, change this if necessary.
Furthermore, the correct region and or chromosome needs to be defined for plotting the matrix, TADs or PCA.
As part of this container all workflows are accessible via the Admin account and available under the
<a target="_parent" href="/workflows/list">workflow list menue</a>.
<h2> Known pitfalls </h2>
Preprocssed SAM/BAM files:
To build the contact matrix the SAM/BAM files need to generated using the --reorder option from bowtie2 / hisat2 to output the SAM/BAM files in the exact same order as in the fastq files. To cover the identical reason, the SAM/BAM file should not be sorted. Please make sure your preprocessed SAM/BAM files fulfill these requirements, if not the creation of a contact matrix with hicBuildMatrix will fail.
We recommend to use BWA-MEM with the Hi-C specific parameters
</p>
<br>
<hr/>
<br>
<p class="lead">
<a target="_blank" class="reference" href="http://galaxyproject.org/">
Galaxy</a> is an open platform for supporting data intensive
research. Galaxy is developed by <a target="_blank" class="reference" href="http://wiki.galaxyproject.org/GalaxyTeam">The Galaxy Team</a>
with the support of <a target="_blank" class="reference" href="https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTORS.md">many contributors</a>.
The Galaxy Docker project is supported by the University of Freiburg, part of de.NBI.
</p>
<footer>
The <a target="_blank" class="reference" href="http://galaxyproject.org/">Galaxy Project</a>
is supported in part by <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>,
<a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>,
<a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>,
<a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>,
<a target="_blank" class="reference" href="http://www.denbi.de">The German Network for Bioinformatics Infrastructure (de.NBI)</a>,
<a target="_blank" class="reference" href="http://www.jhu.edu">Johns Hopkins University</a>,
and <a target="_blank" class="reference" href="http://www.uni-freiburg.de">University of Freiburg</a>.
</footer>
<br>
<br>
</div>
</body>
</html>