# \#visualization **URL:** https://help.galaxyproject.org/tag/visualization/323.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Trackster error? Try IGV instead!](https://help.galaxyproject.org/t/trackster-error-try-igv-instead/4060)
**Author:** [@enten](https://help.galaxyproject.org/u/enten)\ **Replies:** 1\ **Last updated:** [April 14, 2026, 7:43pm UTC](https://help.galaxyproject.org/t/trackster-error-try-igv-instead/4060 "2026-04-14T19:43:17Z")
Hello, I am using BWA to map a yeast WGS on a custom genome that I uploaded in my history. When I try to visualize the mapping using Trackster and picking the custome genome build for the indexing, I get the following … --- ## [Custom genome? How to display in IGV! bigwigs, bams, any coordinate data](https://help.galaxyproject.org/t/custom-genome-how-to-display-in-igv-bigwigs-bams-any-coordinate-data/17376)
**Author:** [@Sherry](https://help.galaxyproject.org/u/Sherry)\ **Replies:** 7\ **Last updated:** [January 30, 2026, 5:39pm UTC](https://help.galaxyproject.org/t/custom-genome-how-to-display-in-igv-bigwigs-bams-any-coordinate-data/17376 "2026-01-30T17:39:41Z")
Hi there, Could anybody tell me why my bigwig file can’t be opened in UCSC browser, but only visualized in IGB or IGV? I know how to open the file in IGB, but personally I just feel the display in UCSC genome browser… --- ## [Multiple Sequence Alignment is not interactive](https://help.galaxyproject.org/t/multiple-sequence-alignment-is-not-interactive/16226)
**Author:** [@Agoston\_Hunya](https://help.galaxyproject.org/u/Agoston_Hunya)\ **Replies:** 2\ **Last updated:** [September 2, 2025, 4:57pm UTC](https://help.galaxyproject.org/t/multiple-sequence-alignment-is-not-interactive/16226 "2025-09-02T16:57:17Z")
Hello! I’ve been trying to visualize a MSA on Galaxy using the Multiple Sequence Alignment under the Visualization tab. When I select my FASTA file, it creates a plot of the alignment but it is non-scrollable and I cann… --- ## [CSV output displays header twice](https://help.galaxyproject.org/t/csv-output-displays-header-twice/15588)
**Author:** [@Paul\_Wolfe](https://help.galaxyproject.org/u/Paul_Wolfe)\ **Replies:** 3\ **Last updated:** [May 30, 2025, 6:04pm UTC](https://help.galaxyproject.org/t/csv-output-displays-header-twice/15588 "2025-05-30T18:04:12Z")
Hello, I have been working on a new tool (reactome\_cli) but have run into what I think is a bug in the CSV display. See the attached image, the header is displayed twice. The CSV itself does not have the header line d… --- ## [plot visualization unavailable](https://help.galaxyproject.org/t/plot-visualization-unavailable/15319)
**Author:** [@Ernesto](https://help.galaxyproject.org/u/Ernesto)\ **Replies:** 1\ **Last updated:** [April 25, 2025, 4:53pm UTC](https://help.galaxyproject.org/t/plot-visualization-unavailable/15319 "2025-04-25T16:53:49Z")
The visualization of images of graphs and PDFs is not available. This is the message displayed on the server: 404 Not Found nginx/1.20.1. any possible solution to this? --- ## [Snpeff Eff tool not loading the graphs in HTML view](https://help.galaxyproject.org/t/snpeff-eff-tool-not-loading-the-graphs-in-html-view/14962)
**Author:** [@Aviral\_Singh\_28](https://help.galaxyproject.org/u/Aviral_Singh_28)\ **Replies:** 1\ **Last updated:** [March 11, 2025, 9:51pm UTC](https://help.galaxyproject.org/t/snpeff-eff-tool-not-loading-the-graphs-in-html-view/14962 "2025-03-11T21:51:30Z")
i have performed the annotation it’s showing the whole result with tables and all but not showing the graphs when trying to load again showing nothing --- ## [Pavian Visualization Tool: Job Info remains "stopped"](https://help.galaxyproject.org/t/pavian-visualization-tool-job-info-remains-stopped/14234)
**Author:** [@bgood07](https://help.galaxyproject.org/u/bgood07)\ **Replies:** 1\ **Last updated:** [December 28, 2024, 9:26pm UTC](https://help.galaxyproject.org/t/pavian-visualization-tool-job-info-remains-stopped/14234 "2024-12-28T21:26:00Z")
Hello, question, I am working on taxonomic profling using Kraken2. I have been able to generate the kraken2 reports on my samples. However, when I try to visualize them using the interactive tool Pavian Visualization, t… --- ## [heat map in beta diversity (Mothur)](https://help.galaxyproject.org/t/heat-map-in-beta-diversity-mothur/14009)
**Author:** [@Shweta.203](https://help.galaxyproject.org/u/Shweta.203)\ **Replies:** 2\ **Last updated:** [December 3, 2024, 6:08pm UTC](https://help.galaxyproject.org/t/heat-map-in-beta-diversity-mothur/14009 "2024-12-03T18:08:56Z")
Hi everyone, I am trying to use Heatmap.sim tool for generating heat maps for beta diversity. The heat map is not being generated, but the svg files were generated, it displays like this Heatmap for input\_dist.dat … --- ## [Unable to run galaxy Ubuntu](https://help.galaxyproject.org/t/unable-to-run-galaxy-ubuntu/12378)
**Author:** [@ajreddys](https://help.galaxyproject.org/u/ajreddys)\ **Replies:** 7\ **Last updated:** [November 19, 2024, 8:02am UTC](https://help.galaxyproject.org/t/unable-to-run-galaxy-ubuntu/12378 "2024-11-19T08:02:09Z")
I have cloned galaxy into my ubuntu machine and when I did sh run.sh this is what I get Traceback (most recent call last): File “”, line 1, in File “/home/aj/Usegalaxy/galaxy/lib/galaxy/util/init.py”, line 54, in i… --- ## [creating a Venn Diagram](https://help.galaxyproject.org/t/creating-a-venn-diagram/13441)
**Author:** [@shubha\_gujjar](https://help.galaxyproject.org/u/shubha_gujjar)\ **Replies:** 1\ **Last updated:** [September 16, 2024, 6:26pm UTC](https://help.galaxyproject.org/t/creating-a-venn-diagram/13441 "2024-09-16T18:26:24Z")
how can i get the venn diagram forthe specific genes --- ## [SVG troubleshooting](https://help.galaxyproject.org/t/svg-troubleshooting/11682)
**Author:** [@chenyw](https://help.galaxyproject.org/u/chenyw)\ **Replies:** 4\ **Last updated:** [July 24, 2024, 1:08pm UTC](https://help.galaxyproject.org/t/svg-troubleshooting/11682 "2024-07-24T13:08:18Z")
Hello, I have similar issues with a different tool, “Visualisation of compounds”. When asked to produce SVG output, an XML text page is shown (at Galaxy.org). I tried it at Galaxy.eu and it shows the SVG graphics correc… --- ## [Error when parsing assembly graph data in Bandage Image](https://help.galaxyproject.org/t/error-when-parsing-assembly-graph-data-in-bandage-image/12784)
**Author:** [@Manuel1](https://help.galaxyproject.org/u/Manuel1)\ **Replies:** 2\ **Last updated:** [June 26, 2024, 7:46am UTC](https://help.galaxyproject.org/t/error-when-parsing-assembly-graph-data-in-bandage-image/12784 "2024-06-26T07:46:55Z")
Dear Galaxy Users, I am new to genome analyses and was running through some of the tutorials to get familiar with the functionalities and workflows in Galaxy. Whilst running through the De Bruijn Graph Assembly tutorial,… --- ## [UCSC link using Galaxy to see RNA seq peaks](https://help.galaxyproject.org/t/ucsc-link-using-galaxy-to-see-rna-seq-peaks/12362)
**Author:** [@rizwan\_rehman\_rehimi](https://help.galaxyproject.org/u/rizwan_rehman_rehimi)\ **Replies:** 1\ **Last updated:** [April 30, 2024, 6:14pm UTC](https://help.galaxyproject.org/t/ucsc-link-using-galaxy-to-see-rna-seq-peaks/12362 "2024-04-30T18:14:30Z")
Dear All, how can I generate the UCSC link using Galaxy to see RNA seq peaks? Thanks in advance Greetings, --- ## [RNA seq Vs Tag Seq](https://help.galaxyproject.org/t/rna-seq-vs-tag-seq/11805)
**Author:** [@Merna](https://help.galaxyproject.org/u/Merna)\ **Replies:** 1\ **Last updated:** [February 29, 2024, 2:20am UTC](https://help.galaxyproject.org/t/rna-seq-vs-tag-seq/11805 "2024-02-29T02:20:42Z")
Hello Everyone, I have some Tag-seq data and i was wondering if i can use the Visualization of RNA-Seq results with heatmap2 tutorial to my data. Would that be accurate or not? --- ## [Rendering svg from galaxy](https://help.galaxyproject.org/t/rendering-svg-from-galaxy/10724)
**Author:** [@droslj](https://help.galaxyproject.org/u/droslj)\ **Replies:** 6\ **Last updated:** [September 14, 2023, 11:45pm UTC](https://help.galaxyproject.org/t/rendering-svg-from-galaxy/10724 "2023-09-14T23:45:55Z")
Hi I am having problems with rendering of svg output. Galaxy interprets this as text. Even if I use browser or some other tool that recognizes svg format, I get graphics, but no text (squares represent text). Is there a… --- ## [Track height in trackster](https://help.galaxyproject.org/t/track-height-in-trackster/11176)
**Author:** [@Richard\_Naiberg](https://help.galaxyproject.org/u/Richard_Naiberg)\ **Replies:** 2\ **Last updated:** [November 20, 2023, 7:14pm UTC](https://help.galaxyproject.org/t/track-height-in-trackster/11176 "2023-11-20T19:14:37Z")
When a load a number of tracks, I can only see a sliver of the output. Here is one view here is another of the same output How can I see them all at the same time? --- ## [Trying to Get Local Galaxy running, but can't open localhost:8080 in browser ERR:CONNECTION\_REFUSED](https://help.galaxyproject.org/t/trying-to-get-local-galaxy-running-but-cant-open-localhost-8080-in-browser-err-connection-refused/4726)
**Author:** [@aroebuck](https://help.galaxyproject.org/u/aroebuck)\ **Replies:** 4\ **Last updated:** [November 6, 2023, 8:06pm UTC](https://help.galaxyproject.org/t/trying-to-get-local-galaxy-running-but-cant-open-localhost-8080-in-browser-err-connection-refused/4726 "2023-11-06T20:06:56Z")
Trying to get a local Galaxy server running - I think I managed to get the right Python (3.6) installed, but I still can’t get Galaxy to open in localhost:8080. I’ve pasted the log below. I tried switching to the python … --- ## [Nucmer plot meaning](https://help.galaxyproject.org/t/nucmer-plot-meaning/10732)
**Author:** [@Jidapha](https://help.galaxyproject.org/u/Jidapha)\ **Replies:** 1\ **Last updated:** [September 5, 2023, 9:01pm UTC](https://help.galaxyproject.org/t/nucmer-plot-meaning/10732 "2023-09-05T21:01:06Z")
Hi, do you know what does parallel lines from nucmer plot means? --- ## [caniuse-lite is outdated error during run.sh build](https://help.galaxyproject.org/t/caniuse-lite-is-outdated-error-during-run-sh-build/10345)
**Author:** [@pjlombardo](https://help.galaxyproject.org/u/pjlombardo)\ **Replies:** 9\ **Last updated:** [August 8, 2023, 8:51pm UTC](https://help.galaxyproject.org/t/caniuse-lite-is-outdated-error-during-run-sh-build/10345 "2023-08-08T20:51:32Z")
Hi all, I’ve been trying for several days to install a local instance of galaxy on a VM running Ubuntu 22.04. I’ve created a local, non-root galaxy user and started a conda virtual environment running python 3.7.6 (alt… --- ## [Troubleshooting Galaxy dataset link-outs to UCSC Genome Browser](https://help.galaxyproject.org/t/troubleshooting-galaxy-dataset-link-outs-to-ucsc-genome-browser/10053)
**Author:** [@justme](https://help.galaxyproject.org/u/justme)\ **Replies:** 6\ **Last updated:** [July 3, 2023, 6:20pm UTC](https://help.galaxyproject.org/t/troubleshooting-galaxy-dataset-link-outs-to-ucsc-genome-browser/10053 "2023-07-03T18:20:06Z")
Hi, Today, the link to UCSC genome browser in the visualization window (bigwig file) has disappeared. How can I visualise my file again in this browser that I prefer above IGB or IGV? I tried: “Build custom track fo… --- ## [MethylDackel, GTN Tutorial Galaxies, and DNA Methylation](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510)
**Author:** [@ntillquist](https://help.galaxyproject.org/u/ntillquist)\ **Replies:** 9\ **Last updated:** [June 20, 2023, 7:01pm UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510 "2023-06-20T19:01:24Z")
I was following the tutorial “DNA Methylation data analysis” and the MethylDackel tool that it says to use for Methylation bias and metric extraction can not be found. I tried to download the tutorial’s workflow and it s… --- ## [Visualization of box plot(jqPlot) problem](https://help.galaxyproject.org/t/visualization-of-box-plot-jqplot-problem/8152)
**Author:** [@Arman\_Kulyyassov](https://help.galaxyproject.org/u/Arman_Kulyyassov)\ **Replies:** 10\ **Last updated:** [June 5, 2023, 7:33pm UTC](https://help.galaxyproject.org/t/visualization-of-box-plot-jqplot-problem/8152 "2023-06-05T19:33:05Z")
Hi Galaxy team! I started training on Label-free data analysis using MaxQuant. I have a problem with “Visualize this data” on the cut tool result. When I selected box plot(jqPlot) it did not visualize data. Instead a… --- ## [Galaxy no longer allows viewing bigwig files in UCSC genome browser](https://help.galaxyproject.org/t/galaxy-no-longer-allows-viewing-bigwig-files-in-ucsc-genome-browser/8804)
**Author:** [@James\_Anderson](https://help.galaxyproject.org/u/James_Anderson)\ **Replies:** 2\ **Last updated:** [October 11, 2022, 11:16pm UTC](https://help.galaxyproject.org/t/galaxy-no-longer-allows-viewing-bigwig-files-in-ucsc-genome-browser/8804 "2022-10-11T23:16:47Z")
Hello, for several years I have been using Galaxy to host my bigwig files, which I then visualize in the UCSC genome browser. Just recently, I have found that Galaxy doesn’t allow this feature anymore. To elaborate: Typi… --- ## [pathview results blank on new run, but rerun works](https://help.galaxyproject.org/t/pathview-results-blank-on-new-run-but-rerun-works/9971)
**Author:** [@Lzprry](https://help.galaxyproject.org/u/Lzprry)\ **Replies:** 3\ **Last updated:** [May 2, 2023, 4:48pm UTC](https://help.galaxyproject.org/t/pathview-results-blank-on-new-run-but-rerun-works/9971 "2023-05-02T16:48:21Z")
Hi, I am trying to run pathview and I am able to rerun an older successful run. But when I use the same files and parameters for a new run, the result is blank. The only difference I can see is the version of R being … --- ## [Volcano plot error](https://help.galaxyproject.org/t/volcano-plot-error/7362)
**Author:** [@CSm](https://help.galaxyproject.org/u/CSm)\ **Replies:** 12\ **Last updated:** [April 24, 2023, 8:01am UTC](https://help.galaxyproject.org/t/volcano-plot-error/7362 "2023-04-24T08:01:08Z")
Dear Galaxy community, I’am new to the Galaxy project. I tried using the Volcano plot tool. Everytime I got th efollowing error message: \[1\] “Header row detected” Error in log10(pvalue) : non-numeric argument to mathem… --- ## [Load function 'load' not found. when loading MSA viewer on usegalaxy.org](https://help.galaxyproject.org/t/load-function-load-not-found-when-loading-msa-viewer-on-usegalaxy-org/8137)
**Author:** [@Peter\_van\_Heusden](https://help.galaxyproject.org/u/Peter_van_Heusden)\ **Replies:** 3\ **Last updated:** [June 10, 2022, 7:37pm UTC](https://help.galaxyproject.org/t/load-function-load-not-found-when-loading-msa-viewer-on-usegalaxy-org/8137 "2022-06-10T19:37:29Z")
I get the following error when trying to load any multiple sequence alignment on .org --- ## [How to visualize HIC data in a circular layout](https://help.galaxyproject.org/t/how-to-visualize-hic-data-in-a-circular-layout/9278)
**Author:** [@Oksanak22](https://help.galaxyproject.org/u/Oksanak22)\ **Replies:** 1\ **Last updated:** [January 14, 2023, 12:04am UTC](https://help.galaxyproject.org/t/how-to-visualize-hic-data-in-a-circular-layout/9278 "2023-01-14T00:04:24Z")
Hello. I have HIC data (.hic and.cool files) and i can’t visualise them in a circular layout. I used “Circos visualizes data in a circular layout” form https://usegalaxy.org/ . Any suggestions or comments? Thank you, … --- ## [kmeans clustering in plotHeatmap](https://help.galaxyproject.org/t/kmeans-clustering-in-plotheatmap/8458)
**Author:** [@dan\_foltz](https://help.galaxyproject.org/u/dan_foltz)\ **Replies:** 1\ **Last updated:** [September 23, 2022, 7:54pm UTC](https://help.galaxyproject.org/t/kmeans-clustering-in-plotheatmap/8458 "2022-09-23T19:54:44Z")
I am trying to create a clustered heat map of Cut and Run data using deeptools (computeMatrix → plotHeatmap). Outside of galaxy the kmeans assignment is simple in plotHeatmap, but I cannot find a way to apply this param… --- ## [Overlapping genelist](https://help.galaxyproject.org/t/overlapping-genelist/8453)
**Author:** [@Jiahui](https://help.galaxyproject.org/u/Jiahui)\ **Replies:** 1\ **Last updated:** [September 21, 2022, 11:47pm UTC](https://help.galaxyproject.org/t/overlapping-genelist/8453 "2022-09-21T23:47:21Z")
Hi all, I have RNA-seq dataset for 3 different cell lines, and I followed the tutorial got the DE genes, I want to compare the overlapping up(/down) regulated genes, is there any tool that I can use to make this overlap… --- ## [Is it possible to include EasyFig in Galaxy?](https://help.galaxyproject.org/t/is-it-possible-to-include-easyfig-in-galaxy/8542)
**Author:** [@carlos.pqc](https://help.galaxyproject.org/u/carlos.pqc)\ **Replies:** 1\ **Last updated:** [August 30, 2022, 5:04pm UTC](https://help.galaxyproject.org/t/is-it-possible-to-include-easyfig-in-galaxy/8542 "2022-08-30T17:04:52Z")
Hello community! I have tried to use EasyFig on Windows and on MacOS but neither of them works. It seems that is a blast issue, but in several forums people are facing the same problem. I used to run EasyFig on my MacOS… [Next page](https://help.galaxyproject.org/tag/visualization/323.md?match_all_tags=true&page=1&tags%5B%5D=visualization)