Question: How to convert GTF format to BED format?
0
gravatar for M K
4.4 years ago by
M K460
United States
M K460 wrote:

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.

 

sequencing rna-seq next-gen • 3.7k views
ADD COMMENTlink written 4.4 years ago by M K460

Hello M K!

Questions similar to yours can already be found at:

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by RamRS22k
1
gravatar for Alex Reynolds
4.4 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

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

ADD COMMENTlink written 4.4 years ago by Alex Reynolds28k
0
gravatar for Devon Ryan
4.4 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

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

ADD COMMENTlink written 4.4 years ago by Devon Ryan90k

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

ADD REPLYlink written 4.4 years ago by M K460
1

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

ADD REPLYlink written 4.4 years ago by Devon Ryan90k

H i 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. 

ADD REPLYlink written 4.4 years ago by M K460

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

ADD REPLYlink written 4.4 years ago by Ann2.2k

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.

ADD REPLYlink written 4.4 years ago by M K460

 

 

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by M K460
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