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Integrated genome browser, how to add exons?

Hi guys, I have a gene of interest, and I've aligned my reads against it using BWA and have presented the alignment (*.bmw) in the integrated genome browser. But I also want to see visualize the exons above the read tracks. Obviously I know the exon locations along the gene and the sequences. How can this be done in integrated genome browser? I've looked through IGV's documentation and could not find it.

Thank you. a

software igv
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written by omer.k • omer.k

Thank you! Few more questions.. Can I generate this file with the standard notepad, and save it as a BED file? Also, I'm aligning against a gene of interest rather than a chromosome. So I guess the line would be?

Gene1 1000 5000 gene1 . + 1000 5000 0 2 250,500, 0,3500
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written by omer.k • omer.k

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This comment should have gone under @Gungor's answer.

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written by GenoMax GenoMax

@omer.k Sure, just make sure you have the correct format. Filename or the extension won't matter but I suggest you keep the extension as .bed, instead of .txt which can be done using Notepad on Windows. However, you should also consider installing a better text editor such as Atom.

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written by Gungor Budak Gungor Budak

@omar.k, for the question related to the line: No, it won't work this way. You can write the gene name to the fourth column and keep the gene's chromosome name in the first column. Otherwise, IGV won't know which chromosome to put your gene/exons on.

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written by Gungor Budak Gungor Budak

1 answer

You just make a BED file for your gene in one line and specify exon locations. For example,

Say your gene starts from chrY position 1000 and ends at chrY position 5000 and has two exons from position 1000 with size 250 and position 4500 with size 500. So the BED file should have the following line;

chrY 1000 5000 gene1 . + 1000 5000 0 2 250,500, 0,3500

These are space separated columns for:

  • Chromosome
  • Start location
  • End location
  • Gene name
  • Some score
  • Strand
  • Thick start (just make it start location)
  • Thick end (just make it end location)
  • Color
  • Item count (number of exons)
  • Item sizes (item count many sizes separated by comma)
  • Item starts (item count many starts relative to start location separated by comma)

And it should look like this:

IGV visualization

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written by Gungor Budak Gungor Budak

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