AB1 file in IGV-help

[Ram Vinay Pandey]

Hi,

I have electropherogram files in AB1 format. 

Is it possible to visualize the .ab1 extension file in IGV?

I want to plot electropherogram in IGV along with genome coordinate (as given in attached image).

any idea is highly appreciated.

File Extension AB1 Description:

The AB1 file extension (generated by Applied Biosystems genome sequencing) is used to store data files. Files with the .ab1 file extension are DNA electropherogram files. The file format is used to store the results of an electrophoresis analysis. The data in files with the file extension .ab1 stores the reactions of DNA against an electric field.

Files with the AB1 file extension contain data describing raw DNA. These files can be generated by a number of scientific instruments. The file extension .ab1 was primarily developed as the default file extension for files created by Applied Biosystems' programs. The file extension AB1 is used to store a graph, which shows the results of an electropherogram. The file also comes with the base sequence of the DNA tested.

many thanks,

Ram

--

Ram Vinay Pandey
Institute of Population Genetics
University of Veterinary Medicine Vienna
Veterinärplatz 1
A-1210 Wien
T: +43-1-25077-4335
Mob:+4368110662526
ramvina...@vetmeduni.ac.at

[James Robinson]

Hi,

This is not possible at this time,  we do not support that format and there is no graphical view.   I will note this as an enhancement request.

-- Jim

<electropherogram.jpg>

[Ram Vinay Pandey]

Hi James,

Many thanks for your quick reply. I hope in next version of IGV we could visualize AB1 files (Electropherogram)

Next, I wanted to integrate IGV in my RNA-SEQ analysis pipeline which I am developing in Python. so is it possible to call IGV within python script and sending reference fasta, GTF and BAM files via command line to IGV?

It would be very helpful, if you could help in this.

thank you,

Ram

--
Ram Vinay Pandey
Institute of Population Genetics
University of Veterinary Medicine Vienna
Veterinärplatz 1
A-1210 Wien
T: +43-1-25077-4335
Mob:+4368110662526
ramvina...@vetmeduni.ac.at

[Cook, Malcolm]

Ram,

 

Wondering what exactly you mean by ‘visualize AB1 files’. 

 

Do you want to visualize the alignments of AB1 sequences to some genome?

 

If so, your problem becomes one of reformatting its output into SAM|BAM format, which IGV can display in the context of the genome.

 

~Malcolm

[Jacob Silterra]

It depends on what you'd like to do. IGV contains a separate utility
called "IGVTools", this can also be downloaded separately. Python can
send commands to the system shell, you could use this to call
IGVTools. See the user guide at
http://www.broadinstitute.org/igv/igvtools for what you can do.

Besides that, IGV can accept some external commands. See
http://www.broadinstitute.org/software/igv/external_control.

-Jacob

--
Jacob Silterra
Software Engineer
Broad Institute

[James Robinson]

I think Jacob covered the possibilities,  I would like to just emphasize the port option.   From the command line you could start IGV on various files, but of course can't control it once started.  Using the port you can.

We might need to add an extension to let you specify the reference fasta through the port, but this would be a minor change.

Jim