Question: Integrated genome browser, how to add exons?
gravatar for omer.k
2.6 years ago by
omer.k40 wrote:

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

igv software • 848 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by omer.k40

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
ADD REPLYlink written 2.6 years ago by omer.k40

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.

ADD REPLYlink written 2.6 years ago by genomax85k

@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.

ADD REPLYlink written 2.6 years ago by Gungor Budak240

@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.

ADD REPLYlink written 2.6 years ago by Gungor Budak240
gravatar for Gungor Budak
2.6 years ago by
Gungor Budak240
Gungor Budak240 wrote:

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

ADD COMMENTlink written 2.6 years ago by Gungor Budak240
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