How to convert GTF format to BED format?

Question

[M K]

Hi All,

I am going to check mapped reads that I got from tophat, and I want to use IGV to look for specific genes names in my data . In my case ,I have to create .genome file in IGV because I used the reference genome and the annotation file from Ensemble .

I tried to creat my .genome file on IGV, I found that in IGV user guide I should have the annotation file as .BED format. so is there any simple tool to convert gtf to bed format.

[Ram]

Hello M K!

Questions similar to yours can already be found at:

• How To Convert Gencode Gtf Into Bed Format ?

Answer 1

[Alex Reynolds]

You can use BEDOPS gtf2bed, e.g., $ gtf2bed < my_data.gtf > my_data.bed

Answer 2

[Devon Ryan]

You can use a GTF file in IGV for the annotation. In fact, that's the most common method.

[M K]

When I used GTF in IGV it doesn't show any thing. That's why I trying to follow the user guide on IGV

[Devon Ryan]

That's unusual. I've done this exact thing before and not had issues. Perhaps something is wonky with the GTF.

[M K]

Hi Ryan,

As I said above, I downloaded both of the reference genome and the annotation file from Ensemble. So I don't think there is any problem with the GTF file. Also, I got a high rate for mapping using tophat.

[Ann]

It's possible IGV doesn't recognize the chromosome names.

[M K]

Could you please explain this point to me. the annotation file that I used just has the chromosome number only without Chr. Also the same problem happened when I used the default hg19 in IGV.