add link to references (6a40895f) · Commits · github_fork / Universc

README.Rmd

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		@@ -128,6 +128,13 @@ Note that you need to run the shell commands given in a unix-like command-line i

		If you run into problems installing or running `launch_universc.sh` please don't hesistate to contact us via email or GitHub.

		### Graphical application Users

		We also provide a graphical user interface (GUI) based application to run the Docker [image](#Docker). Please install Docker as described above and pull our `tomkellygenetics/universc:latest` image using either the docker command-line interface (CLI) or the docker graphical application.

		Once you have a docker image installed on your system, you can run the applicable binary available here:

		[https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_Release/](https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_Release/)

		## Purpose

		@@ -944,6 +951,12 @@ make reference
		cd ../../..
		```

		#### Pre-generated References

		For convenience we provide pre-generated references for the human genome and various model species available for download:

		[https://genomec.gsc.riken.jp/gerg/UniverSC/Premade_references/](https://genomec.gsc.riken.jp/gerg/UniverSC/Premade_references/)

		#### Custom Cell Ranger references

		It is also possible to generate a custom reference for any genome provided you have

README.html

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		<p>If you are a beginner bioinformatician or wish to run this on a local computer (Mac or Windows), no problem! We provide a "docker" image containing everything needed to run it without installing the software needed. All you need to do is install <a href="https://docs.docker.com/desktop/">docker</a> and follow our guide to use the <a href="#Docker">image</a>. This comes bundled with all the compatible versions needed to run it.</p>
		<p>Note that you need to run the shell commands given in a unix-like command-line interface (the "Terminal" application on Mac or Linux systems). Many shells are supported but we recommend the "bash" shell for beginners (this is the default on most systems). Windows 10 includes a <a href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">subsystem</a> to run <code>bash</code>. If this is too complicated, you can open a Linux environment (Ubuntu) in docker by following our instructions. Then you can enter bash commands into the terminal opened by docker.</p>
		<p>If you run into problems installing or running <code>launch_universc.sh</code> please don't hesistate to contact us via email or GitHub.</p>
		<h3 id="graphical-application-users">Graphical application Users</h3>
		<p>We also provide a graphical user interface (GUI) based application to run the Docker <a href="#Docker">image</a>. Please install Docker as described above and pull our <code>tomkellygenetics/universc:latest</code> image using either the docker command-line interface (CLI) or the docker graphical application.</p>
		<p>Once you have a docker image installed on your system, you can run the applicable binary available here:</p>
		<p><a href="https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_Release/" class="uri">https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_Release/</a></p>
		<h2 id="purpose">Purpose</h2>
		<p>We've developed a bash script that will run Cell Ranger on FASTQ files for these technologies. See below for details on how to use it.</p>
		<p>If you use this tool, please <a href="#Citation">cite</a> to acknowledge the efforts of the authors. You can report problems and request new features to the maintainers with and <a href="#Issues">issue</a> on GitHub. Details on how to <a href="#Install">install</a> and <a href="#Usage">run</a> are provided below. Please see the <a href="#Help">help</a> and <a href="#Examples">examples</a> to try solve your problem before submitting an issue.</p>
		@@ -442,6 +446,9 @@ fi</code></pre>
		make clean
		make reference
		cd ../../..</code></pre>
		<h4 id="pre-generated-references">Pre-generated References</h4>
		<p>For convenience we provide pre-generated references for the human genome and various model species available for download:</p>
		<p><a href="https://genomec.gsc.riken.jp/gerg/UniverSC/Premade_references/" class="uri">https://genomec.gsc.riken.jp/gerg/UniverSC/Premade_references/</a></p>
		<h4 id="custom-cell-ranger-references">Custom Cell Ranger references</h4>
		<p>It is also possible to generate a custom reference for any genome provided you have a FASTQ genome reference file and a GTF/GFF3 annotation file. Please ensure that the chromosomes match between the FASTA headers and the chromosome column (1st) of the GTF/GFF3 file.</p>
		<p>The <code>gffread</code> function includes with the <a href="http://cole-trapnell-lab.github.io/cufflinks/file_formats/#the-gffread-utility">cufflinks</a> utility can convert to gtf. For example:</p>

README.md

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		@@ -6,7 +6,7 @@ affiliations:
		index: 1
		- name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"
		index: 2
		date: "Sunday 26 September 2021"
		date: "Monday 11 October 2021"
		output:
		prettydoc::html_pretty:
		theme: cayman
		@@ -128,6 +128,13 @@ Note that you need to run the shell commands given in a unix-like command-line i

		If you run into problems installing or running `launch_universc.sh` please don't hesistate to contact us via email or GitHub.

		### Graphical application Users

		We also provide a graphical user interface (GUI) based application to run the Docker [image](#Docker). Please install Docker as described above and pull our `tomkellygenetics/universc:latest` image using either the docker command-line interface (CLI) or the docker graphical application.

		Once you have a docker image installed on your system, you can run the applicable binary available here:

		[https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_Release/](https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_Release/)

		## Purpose

		@@ -944,6 +951,12 @@ make reference
		cd ../../..
		```

		#### Pre-generated References

		For convenience we provide pre-generated references for the human genome and various model species available for download:

		[https://genomec.gsc.riken.jp/gerg/UniverSC/Premade_references/](https://genomec.gsc.riken.jp/gerg/UniverSC/Premade_references/)

		#### Custom Cell Ranger references

		It is also possible to generate a custom reference for any genome provided you have

launch_universc.sh

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		@@ -195,6 +195,9 @@ Mandatory arguments to long options are mandatory for short options too.
		-i, --id ID A unique run id, used to name output folder
		-d, --description TEXT Sample description to embed in output files.
		-r, --reference DIR Path of directory containing 10x-compatible reference.
		Available here the human genome and various model species:
		https://genomec.gsc.riken.jp/gerg/UniverSC/Premade_references/

		-t, --technology PLATFORM Name of technology used to generate data.
		Supported technologies:
		10x Genomics (version automatically detected): 10x, chromium

man/launch_universc.sh

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		@@ -189,6 +189,12 @@ Provides a conversion script to run multiple technologies and custom libraries w
		See Cell Ranger documentation on how to generate custom "transcriptomes" or
		download human and mouse references from the 10x Genomics website.

		For convenience we provide pre-generated references for the human genome and
		various model species available for download:

		https://genomec.gsc.riken.jp/gerg/UniverSC/Premade_references/


		-t, --technology PLATFORM
		Name of technology used to generate data.

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