text: user711: I was following a tutorial on "Tuxedo Genome Guided Transcriptome Assembly Workshop" and was wondering how to interpret the following:
  
  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?
  
  user77: 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.
  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.
  
original_text: 711: <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.stack.imgur.com/xfFmi.png" rel="noreferrer"><img src="https://i.stack.imgur.com/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>
   77: <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>
  