Comparing two sequences in IGV

[Shakti R]

Hi all,

I'm using IGV Js 1.0.9 (but I did'nt find a way to resolve my problem in the desktop version either).

My problem is that it does not seem possible to load two Fasta sequences at once in the same IGV panel.

So my question is of course : is it possible to compare two Fasta in IGV ?
If not, would you know any tool that can (in particular javascript tool that can be embedded in a HTML page) ?


Best regards and Thank you in advance !

S.

[Irene Bassano]

you can use Artemis comparison tool https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

not sure if on IGV you can upload to genomes (=fatsa)?

ib

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[James Robinson]

Hi,  you can't do that with igv.js.   To compare two sequences you must first align them, otherwise what are you comparing?  See the Artemis tool listed above.   Also,  the UCSC Multiple Alignment tools might be useful.  

On Tue, May 22, 2018 at 11:38 AM, Irene Bassano <ibs...@gmail.com> wrote:

you can use Artemis comparison tool https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

not sure if on IGV you can upload to genomes (=fatsa)?

ib

On May 22, 2018, at 4:36 PM, Shakti R <shaktir...@gmail.com> wrote:

Hi all,

I'm using IGV Js 1.0.9 (but I did'nt find a way to resolve my problem in the desktop version either).

My problem is that it does not seem possible to load two Fasta sequences at once in the same IGV panel.

So my question is of course : is it possible to compare two Fasta in IGV ?
If not, would you know any tool that can (in particular javascript tool that can be embedded in a HTML page) ?


Best regards and Thank you in advance !

S.

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[Shakti R]

Hello,

First of all, thanks for the answers !

In fact, the two sequences are already aligned in MSA multi-alignment format and converted to Fasta. These sequences corresponds to two HLA alleles references (see attachment : A*01:01:01 and A*02:01:01).

Is there a visualization tool that can load these sequences and highlight the differences ? Also, we would like to add information tracks such as amino acid conversion, regions specified in a bed file format (exons/introns), and maybe other useful informations (for example coverage)...

Thanks,

S.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BptG5Jopcqc3%2BD9kJfZP9w74EZvFrx37oe7wKk%3DvFYJ5LQ%40mail.gmail.com.

[Shakti R]

The sequences file !

S.

[James Robinson]

Hi, what you are describing doesn't make sense to me.   You cannot "convert" MSA or any other alignment format to fasta without loosing the alignment information.   A fasta file is just a sequence.   An alignment describes how one sequence "aligns" to another, including relative positions, gaps, and insertions.   You cannot represent an alignment with a fasta alone.

However, to answer your question I don't know of any tool that can do what you describe.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CANbhdN6mxvpkj7hNCt2F2NUf7UKL40dH5uoFELekK_3n1hOjew%40mail.gmail.com.

[Tgrandis]

Hello: 

For what it is worth, to visualise the alignment, identify differences and convert to amino acid sequences try the aliview programme (view - highlight non-consensus). download from
http://ormbunkar.se/aliview/ 

Hugo

On Thursday, 24 May 2018 15:56:37 UTC+7, Shakti R wrote:

Hello,

First of all, thanks for the answers !

In fact, the two sequences are already aligned in MSA multi-alignment format and converted to Fasta. These sequences corresponds to two HLA alleles references (see attachment : A*01:01:01 and A*02:01:01).

Is there a visualization tool that can load these sequences and highlight the differences ? Also, we would like to add information tracks such as amino acid conversion, regions specified in a bed file format (exons/introns), and maybe other useful informations (for example coverage)...

Thanks,

S.

2018-05-22 21:13 GMT+02:00 James Robinson <jrob...@broadinstitute.org>:

Hi,  you can't do that with igv.js.   To compare two sequences you must first align them, otherwise what are you comparing?  See the Artemis tool listed above.   Also,  the UCSC Multiple Alignment tools might be useful.  

On Tue, May 22, 2018 at 11:38 AM, Irene Bassano <ibs...@gmail.com> wrote:

you can use Artemis comparison tool https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

not sure if on IGV you can upload to genomes (=fatsa)?

ib

On May 22, 2018, at 4:36 PM, Shakti R <shaktir...@gmail.com> wrote:

Hi all,

I'm using IGV Js 1.0.9 (but I did'nt find a way to resolve my problem in the desktop version either).

My problem is that it does not seem possible to load two Fasta sequences at once in the same IGV panel.

So my question is of course : is it possible to compare two Fasta in IGV ?
If not, would you know any tool that can (in particular javascript tool that can be embedded in a HTML page) ?


Best regards and Thank you in advance !

S.

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[Shakti R]

Hello,

Aliview does allow to view the sequences, that's a start :)

To answer James message, the general idea is that we initially have paired FASTQ files. Aligment , variant calling, etc, provide BAM and other files with the informations about coverage, etc. For a particular sample, we wanted to visualize two different alleles and compare them. Just using the generated BAM files was not a solution, since it is not possible to view the two alleles at the same time in the IGV track. That's why it seemed interesting to try to use the two alleles sequences in Fasta format as initial tracks in a viewer, then adding the other informations about coverage etc (these informations being indeed available upstream, to be parsed and exported in any format needed for the tool, csv, bed, bigwig...).

But it seems it is a bit too convoluted, anyway thanks again for your help.

S.

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