Body: <p>We have done some RNA-Seq on Arabidopsis T-DNA lines and mapped the reads on to Arabidopsis genome. Now we wanted to confirm the T-DNA deletion of those lines by loading them on IGV. As a control we also wanted to load T-DNA lines as tracks on IGV to make sure that the T-DNA lines we chose were correct. I am wondering where can i get bam files for those confirmed T-DNA lines?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-24T09:10:53.570Z
Comments.Text: Sorry I might be missing something. You mentioned mapping the reads onto the genome. The output is a bam file right? You can just create an index for it and load it into IGV
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-24T20:00:14.003Z
Comments.Text: Are you asking how to see the location and names of all the T-DNA lines, like shown [here](http://signal.salk.edu/cgi-bin/tdnaexpress)?
Comments.UserDisplayName: Lynn
Tags: <sam><visualization><transcriptome><igv>
Title: How to visualise /add Arabidopsis T-DNA Lines As Tracks On IGV
ThreadText: # How to visualise /add Arabidopsis T-DNA Lines As Tracks On IGV
  
  (Asked by: username_0 on 2019-10-24)
  
  We have done some RNA-Seq on Arabidopsis T-DNA lines and mapped the reads on to Arabidopsis genome. Now we wanted to confirm the T-DNA deletion of those lines by loading them on IGV. As a control we also wanted to load T-DNA lines as tracks on IGV to make sure that the T-DNA lines we chose were correct. I am wondering where can i get bam files for those confirmed T-DNA lines?
  
  **Tags:** sam, visualization, transcriptome, igv
  
  > **Comments:**
  > **username_1**: Sorry I might be missing something. You mentioned mapping the reads onto the genome. The output is a bam file right? You can just create an index for it and load it into IGV  
  > **username_2**: Are you asking how to see the location and names of all the T-DNA lines, like shown [here](http://signal.salk.edu/cgi-bin/tdnaexpress)?  
  
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  ## 0 answers
  
  