IGV load custom GTF

[Daniel Fernandez]

 Hi,

I have a custom GTF file that I created from merging: UCSC, ensembl, retro genes and functional RNAs annotations.  I'd like to load this file into IGV, but I get a warning that is not 'indexed'.  Then I try to go ahead and load it into IGV but it wait's forever and eventually crashes.

I read about it and seems the best way to go would be to transform it to bed and then index it.  Thus my questions:

(1) Do you know what's the best way to transform a customized GTF to bed, sort it and index it such that it can be visualized as an annotation, much like the refseq track?

(2) I am using the IGV exome-view feature.  Would the new IGV version with the exome-view recognize such custom bed annotation file?

Please let me know if you can help me here.

Happy Holidays!

Daniel F. 

[Jim Robinson]

Hi,

You do not have to convert it to bed, you can index a GTF file.    You do need to sort it,  you can do that with igvtools.    You can also index it with "tabix".

How large is the gtf file?

Jim

[Jim Robinson]

Sorry, one more question.  I assume the extension is ".gtf",  is it? 

On Monday, December 23, 2013 5:04:18 PM UTC-5, Daniel Fernandez wrote:

[Daniel Fernandez]

Hi Jim, the problem has been solved, I did exactly as you recommended and it worked perfectly fine for my custom GTF.

Just as a side note:  In the igvtools documentation official site it says that sort and index only supports (Supported input file formats: .cn, .igv, .sam, .aligned, .psl, .bed, and .vcf). Shouldn't GTF should also be there or is kind of 'under your own risk' thing?

Thank you very much.

[Jim Robinson]

Thanks for pointing that out, the doc is out-of-date.  We'll correct.   Also, gff should be listed.

Jim

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[Daniel Fernandez]

Great, thanks Jim.  Btw, IGV rocks ;-)

[Roberto Ruiz-Cordero]

Hi,

How can I enable the exome-view feature in IGV version 2.3? Thanks

[James Robinson]

Hi Roberto,

That feature was never formally released,  got very little use,  and has been removed.   It might be brought back in a different form for release 3.0 early next year.   In the meantime, it is available in version 2.3.35 which you can get from the archive

Mac:  http://data.broadinstitute.org/igv/projects/downloads/IGV_2.3.35.app.zip

Others: http://data.broadinstitute.org/igv/projects/downloads/IGV_2.3.35.zip

Jim

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[Roberto Ruiz-Cordero]

Thank you very much for getting back to me so quick.

I happen to really need this feature for a particular assay that we are developing. It will come in very handy.

Thanks again!

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[Roberto Ruiz-Cordero]

Is it supposed to appear as a click-on button in the tool bar or do I need to enable it in preferences or something?

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[James Robinson]

Oh yes, sorry,  are you using the Mac app or the binary distribution?   

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[Roberto Ruiz-Cordero]

Sorry for the delay

I downloaded and opened the file in a PC, so I guess binary distribution

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[V. Chen]

I was able to launch version 2.3.35. Where can I enable the Exome viewing? Thanks!

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[James Robinson]

Open the "igv.bat" file in a text editor and change -Dproduction=true  -Ddevelopment=true

Also, assuming you have 64-bit Java you might also give it more memory by changing, for example  -Xmx2000m  to -Xmx2g   (for 2 gigabytes).

There is another way to get an exome like view in IGV 2.3.97 by using "gene lists".  A gene list is not restricted to genes,  you can define a gene list as a bed file of exons for example.  This file can then be used with "gene list view".   You might consider creating a separate bed file for each transcript you want to view.  See http://software.broadinstitute.org/software/igv/gene_list_view  for more details.    

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[James Robinson]

See my response in this same thread.  Note that this is not a supported feature,  you might consider the "gene list" option if you have just a few locations you want to view in this way.  

[Roberto Ruiz-Cordero]

Ok, thank you very much for your help!

Best,

Roberto

On Tue, Sep 12, 2017 at 1:00 PM, James Robinson <jrob...@broadinstitute.org> wrote:

See my response in this same thread.  Note that this is not a supported feature,  you might consider the "gene list" option if you have just a few locations you want to view in this way.  

I was able to launch version 2.3.35. Where can I enable the Exome viewing? Thanks!

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[Xingliang Zhu]

Seems it doesn't work for me. I sorted the files by bedtools and indexed by IGV, there is no response. I also tried the tabix -p gtf XXX.gtf.gz, when I loaded it to igv, the IGV said cannot load fasta files. So strange. Is there any clear steps that I can index the gtf files?

[igv-help]

Are you loading the file from the "File" menu?  I can't help you without more details, your question is very generic.   See the information message at the top of the google groups page for the type of information we need.