From 97b1a26883e3a4e863760947f67e38dec692796c Mon Sep 17 00:00:00 2001 From: Yassin Khalifa Date: Tue, 7 Nov 2023 20:54:29 -0500 Subject: [PATCH] content for advanced genomics > genome-browser --- .../genome-browser.md | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) diff --git a/docs/advanced-genomics-support/genome-browser.md b/docs/advanced-genomics-support/genome-browser.md index 00b8bd5..245b427 100644 --- a/docs/advanced-genomics-support/genome-browser.md +++ b/docs/advanced-genomics-support/genome-browser.md @@ -1 +1,72 @@ # Genome Browser + +IGV +--- + +The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. The original IGV is a Java desktop application. You can run IGV as a VNC application through Open Ondemand. + +Logon ondemand.htc.crc.pitt.edu. Click Interactive Apps -> IGV on htc: + +![](../_assets/img/advanced-genomics-support/igv-1.png) + +Select IGV version, Number of Hours and Number of cores. Click Launch: + +![](../_assets/img/advanced-genomics-support/igv-1_0.png) + +Choose your genome at the top left cornet. I have selected Human (hg38). File -> Load from File... and navigate to your CRC folder. In the screenshot, I have navigated to ```/bgfs/genomics/fangping/nf-core-rnaseq/results/star/bigwig```, and selected 6 bigWig files. + +![](../_assets/img/advanced-genomics-support/igv-2_0.png) + +Type a gene name in top middle text field. I have used GAPDH. + +![](../_assets/img/advanced-genomics-support/igv-4.png) + +IGV\_webapp +----------- + +The IGV-Web app is a pure-client "genome browser" application based on igv.js. IGV-web is a web application. + +Logon ondemand.htc.crc.pitt.edu. Click Genomics Apps -> IGV webapp: + +![](../_assets/img/advanced-genomics-support/igv-2.png) + +Select IGV webapp version, Number of cores and Number of hours. Click Launch: + +![](../_assets/img/advanced-genomics-support/igvweb-1.png) + +This will launch IGV-webapp using a shared node on the htc cluster. + +![](../_assets/img/advanced-genomics-support/igvweb-2.png) + +Choose your genome at the top left corner. To add files on CRC storage as track, select Tracks -> URL ... Get the absolute path of your file, for example, + +```/bgfs/genomics/fangping/nf-core-rnaseq/results/star/bigwig/scCTRL_TGFb1_R1.bigWig```, + +then add data in front. Use that address, i.e., + +```data/bgfs/genomics/fangping/nf-core-rnaseq/results/star/bigwig/scCTRL_TGFb1_R1.bigWig```, + +as Track URL. + +![](../_assets/img/advanced-genomics-support/igvweb-3.png) + +When track has index, you should provide Index URL. For example, bam file /bgfs/genomics/fangping/nf-core-rnaseq/results/star/scCTRL\_TGFb1\_R1.markdup.sorted.bam and its index file /bgfs/genomics/fangping/nf-core-rnaseq/results/star/scCTRL\_TGFb1\_R1.markdup.sorted.bam.bai. You should use: + +Track URL: ```data/bgfs/genomics/fangping/nf-core-rnaseq/results/star/scCTRL_TGFb1_R1.markdup.sorted.bam``` +Index URL: ```data/bgfs/genomics/fangping/nf-core-rnaseq/results/star/scCTRL_TGFb1_R1.markdup.sorted.bam.bai``` + +![](../_assets/img/advanced-genomics-support/igvweb-4.png) + +Type a gene name in top middle text field. I have used GAPDH. + +![](../_assets/img/advanced-genomics-support/igvweb-5.png) + +To save and share the session, choose Session -> Save ...., and save the json file to your local computer. + +![](../_assets/img/advanced-genomics-support/igvweb-6.png) + +You can send this json file to your collaborator to reproduce the IGV session. Choose Session -> Local File ... to load the session. + +![](../_assets/img/advanced-genomics-support/igvweb-7.png) + +You can upload [this file](../_assets/img/advanced-genomics-support/igv-webapp-session.json) to generate the above session. \ No newline at end of file