Answers.Body: <p>You can use UCSC genome browser, which supports custom genome sequence and annotation. Specifically, one needs to create a <a href="https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html" rel="nofollow noreferrer">Track Hub</a> to hold genomes and annotations. </p>
  
  <p>Here is an example: </p>
  
  <blockquote>
    <p><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt&amp;db=hub_129615_cl_v0.8.2" rel="nofollow noreferrer">http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt&amp;db=hub_129615_cl_v0.8.2</a></p>
  </blockquote>
  
  <p>And here is the corresponding <a href="http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt" rel="nofollow noreferrer">hub.txt</a> file holding the metadata, and URLs to actual fasta, bigWig and bigBed files.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-12T19:24:45.873Z
Answers.LastActivityDate: 2018-10-12T19:24:45.873Z
Answers.UserDisplayName: Yu Fu
Body: <p><strong>Background</strong></p>
  
  <p>We want to be able to load (or request) data for a genome including the sequence and gene annotation (bacteria). Then, we want to load our own annotation which should be displayed as a line plot:</p>
  
  <pre><code>position score
  1        5
  2        6
  etc.
  </code></pre>
  
  <p>Where each position corresponds to the position in the genome (i.e. FASTA).
  Something like this: </p>
  
  <p><a href="https://i.sstatic.net/QWfgP.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/QWfgP.png" alt="enter image description here"></a></p>
  
  <p><strong>Question</strong></p>
  
  <p>Is there a tool that can load a genome sequence, gene annotation, and a position ~ score file, which can be displayed as a line plot? </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-11T13:09:15.937Z
Comments.Text: Welcome to the site. In order to suggest a good alternative could you comment what do you need this tool for? Why do you need to display the gene annotation? What is the problem with IGV ? (I found the sentence a bit confusing, perhaps if you rephrase it I'll understand it)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-11T13:32:33.250Z
Comments.Text: I thought I was clear regarding what I need it for: uploading genome + annotation + own data (position + score). Why gene annotation? Because we want to look whether the the line plot we upload differs between genes and intergenic regions. Just similar as a GC plot beneath the genes and intergenic regions but then with own supplied scores per position. Indeed, I forgot a word in my sentence about IGV @Llopis
Comments.UserDisplayName: KingBoomie
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-11T14:16:27.670Z
Comments.Text: I don't find this question useful. It only helps people who find IGV ugly. Also you don't seem to have researched for other options like [IGB](https://bioviz.org/). Have a nice day!
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-11T15:07:33.423Z
Comments.Text: A local tool is fine, with upload I meant uploading it to a tool (perhaps not the best word choice). The screenshot is from a tool which only visualizes a Listeria genome (no other bacteria), but I liked the interface. Currently I'm trying to use IGB @terdon
Comments.UserDisplayName: KingBoomie
Tags: <genome><sequence-analysis><visualization>
Title: Tool to show DNA sequence and allowing upload of own graph data
ThreadText: # Tool to show DNA sequence and allowing upload of own graph data
  
  (Asked by: username_0 on 2018-10-11)
  
  **Background**
  
  We want to be able to load (or request) data for a genome including the sequence and gene annotation (bacteria). Then, we want to load our own annotation which should be displayed as a line plot:
  
  ```
  position score
  1        5
  2        6
  etc.
  
  ```
  
  Where each position corresponds to the position in the genome (i.e. FASTA).
  Something like this:
  
  [![enter image description here](https://i.sstatic.net/QWfgP.png)](https://i.sstatic.net/QWfgP.png)
  
  **Question**
  
  Is there a tool that can load a genome sequence, gene annotation, and a position ~ score file, which can be displayed as a line plot?
  
  **Tags:** genome, sequence-analysis, visualization
  
  > **Comments:**
  > **username_1**: Welcome to the site. In order to suggest a good alternative could you comment what do you need this tool for? Why do you need to display the gene annotation? What is the problem with IGV ? (I found the sentence a bit confusing, perhaps if you rephrase it I'll understand it)  
  > **username_0**: I thought I was clear regarding what I need it for: uploading genome + annotation + own data (position + score). Why gene annotation? Because we want to look whether the the line plot we upload differs between genes and intergenic regions. Just similar as a GC plot beneath the genes and intergenic regions but then with own supplied scores per position. Indeed, I forgot a word in my sentence about IGV @Llopis  
  > **username_1**: I don't find this question useful. It only helps people who find IGV ugly. Also you don't seem to have researched for other options like [IGB](https://bioviz.org/). Have a nice day!  
  > **username_0**: A local tool is fine, with upload I meant uploading it to a tool (perhaps not the best word choice). The screenshot is from a tool which only visualizes a Listeria genome (no other bacteria), but I liked the interface. Currently I'm trying to use IGB @terdon  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-10-12. Score: 1
  
  You can use UCSC genome browser, which supports custom genome sequence and annotation. Specifically, one needs to create a [Track Hub](https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html) to hold genomes and annotations.
  
  Here is an example:
  
  > <http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt&db=hub_129615_cl_v0.8.2>
  
  And here is the corresponding [hub.txt](http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt) file holding the metadata, and URLs to actual fasta, bigWig and bigBed files.
  
  
  ---
  
  