Answers.Body: <p>You've apparently colored your alignments by read strand. In this case, red indicates "+ (watson) strand" and blue indicates "- (strand) strand". This strand association is determined by the orientation of read #1 in a pair (or just "the read" if you have single-end data). This isn't actually documented in the user manual, but you can find one of the Broad institute software engineers <a href="https://groups.google.com/forum/#!searchin/igv-help/strand$20color%7Csort:relevance/igv-help/YiVzwnUuOZM/sUHc4V1OXZUJ" rel="noreferrer">replying here</a>.</p>
  
  <p>Your next question is likely why the color of the reads and the orientation of the genes are opposite of each other. This is because in modern directional protocols, read #2 in a pair matches the orientation of the gene from which it arose.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-06T02:41:43.923Z
Answers.Text: Thank you for your reply. I'm not sure I understand what you're referring to by read #1 and read #2 based on the picture I attached.
Answers.UserDisplayName: AlwaysTrying44
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-06T06:54:58.157Z
Answers.Text: Ignore that part if you don't understand it. The direct answer to your question is that the colors represent the strand from which the reads arose.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-05T22:21:56.613Z
Answers.LastActivityDate: 2017-09-05T22:21:56.613Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I was following a tutorial on "Tuxedo Genome Guided Transcriptome Assembly Workshop" and was wondering how to interpret the following:</p>
  
  <p><a href="https://i.sstatic.net/xfFmi.png" rel="noreferrer"><img src="https://i.sstatic.net/xfFmi.png" alt="enter image description here"></a></p>
  
  <p>From what I understand from 'Color Legends', the color blue represents something that is below normal and red represents something that is above normal.</p>
  
  <p>Also, my understanding is that merged.gtf is the reconstructed transcript and genes.bed is the reference. They look to be similar for the most part, but seems to have breaks between. What's the appropriate way of interpreting this result?</p>
  
Tags: <rna-seq><phylogenetics><visualization>
Title: Interpreting Intergrative Genomic Viewer (IGV)
ThreadText: # Interpreting Intergrative Genomic Viewer (IGV)
  
  (Asked by: username_0 on 2017-09-05)
  
  I was following a tutorial on "Tuxedo Genome Guided Transcriptome Assembly Workshop" and was wondering how to interpret the following:
  
  [![enter image description here](https://i.sstatic.net/xfFmi.png)](https://i.sstatic.net/xfFmi.png)
  
  From what I understand from 'Color Legends', the color blue represents something that is below normal and red represents something that is above normal.
  
  Also, my understanding is that merged.gtf is the reconstructed transcript and genes.bed is the reference. They look to be similar for the most part, but seems to have breaks between. What's the appropriate way of interpreting this result?
  
  **Tags:** rna-seq, phylogenetics, visualization
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-09-05. Score: 6
  
  You've apparently colored your alignments by read strand. In this case, red indicates "+ (watson) strand" and blue indicates "- (strand) strand". This strand association is determined by the orientation of read #1 in a pair (or just "the read" if you have single-end data). This isn't actually documented in the user manual, but you can find one of the Broad institute software engineers [replying here](https://groups.google.com/forum/#!searchin/igv-help/strand$20color%7Csort:relevance/igv-help/YiVzwnUuOZM/sUHc4V1OXZUJ).
  
  Your next question is likely why the color of the reads and the orientation of the genes are opposite of each other. This is because in modern directional protocols, read #2 in a pair matches the orientation of the gene from which it arose.
  
  > **Comments:**
  > **username_0**: Thank you for your reply. I'm not sure I understand what you're referring to by read #1 and read #2 based on the picture I attached.  
  > **username_1**: Ignore that part if you don't understand it. The direct answer to your question is that the colors represent the strand from which the reads arose.  
  
  ---
  
  