
The included files are provided to demonstrate the ability of IGV to display
RNA structure models and chemical reactivity profiles.


Instructions
============

IGV is freely available for download at https://broadinstitute.org/igv/


HIV-1 RNA genome
----------------

1. Start IGV
2. Load the provided HIV genome. Click the menu item 
     "Genomes"->"Load Genome From File..."
     and select the file HIV/HIV-1_NL4-3.fa
3. Load gene and RNA feature annotations. Click the menu item
     "File"->"Load From File..."
     and select HIV/HIV_genes.gff3 and HIV/HIV_RNA_features.gff3
4. Expand these tracks vertically. Right-click on each track name on the left 
   and select "Expanded"
5. Load an example SHAPE reactivity profile (HIV/HIV.map) and a base pairing
     probability structure model (HIV/HIV.dp). Click the menu item 
     "File"->"Load From File..."
     and select HIV/HIV.map and HIV/HIV.dp
6. Click "Continue" for both dialog boxes that pop up. (There is only one IGV
     "chromosome" - the HIV RNA genome, and there is no need to offset
     coordinates or switch strand.)
7. [Optional] Adjust the vertical data range for the SHAPE reactivity track. 
     Right-click the MaP track name on the left, select
     "Set Data Range...",
     set Min to 0, Max to 4, and click "Continue".
8. [Optional] Reorder tracks by clicking and dragging their names on the left.


E. coli transcripts
-------------------

tmRNA

 1. Load the E. coli genome. Click the menu item
      "Genomes"->"Load Genome From Server..."
      and select "E. coli K-12 MG1655 (U00096.2)"
 2. Load a tmRNA structure model. Click 
      "File"->"Load From File..."
      and select E_coli/tmRNA.dbn or E_coli/tmRNA.ct
 3. In the dialog popup, change the start location from 1 to 2753615, and 
      click "Continue".
 4. Load a tmRNA SHAPE reactivity profile with the same process.
 5. Zoom to the tmRNA gene by entering "tmRNA" into the main search bar and 
      clicking Go or pressing Enter.

glyQ-glyS

 1. Load estimated transcript pairing probabilities by clicking 
      "File"->"Load From File..."
      and selecting E_coli/3720340-3723376_reverse_strand.dp
 2. In the conversion dialog, change the start location to 3720340 and change
      the strand to Reverse. Click "Continue".
 3. Browse to the transcript location by entering the location 
      "U00096.2:3,720,340-3,723,376" or the tag "b3559" in the navigation bar.




