Re: Searching other feature in JBrowse

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Re: Searching other feature in JBrowse

Seyed Ahmad Mousavi
Dear Hans and friends,

As you could see in attached picture my sequences in JBrowse start with e.g "sp|A6NHN0|OTOL1_HUMAN."  I wanted to search part of this accession (like otol1 ) in search box, which one of the following way is possible:

1- Adding gene symbol to this sequences by another file?
2- Or, Should I change the names of sequences in GFF file (e.g instead of "sp|A6NHN0|OTOL1_HUMAN" > "OTOL1")?

I appreciate your helps.

Respectfully,
Ahmad

On Mon, Jul 18, 2016 at 11:34 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:
Hi friends,

I have installed JBrowse on my server and I added fasta file (contains > 70k scaffolds ) and a GFF file in JBrowse. Also, I run generate-names.pl script in Jbrowse. Which I just could search scaffold or contig names in it.

But as you know GFF files has other features like gene symbol, which is not search-able even after running  generate-names.pl.

My question is how can I add other features like gene symbol along with my contigs name?

I appreciate your helps.

Kind regards,
Ahmad


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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: Searching other feature in JBrowse

Saari, Travis

Hi Ahmad,

 

You can do it that way, but another way which preserves your ID’s would be to add a Symbol tag to the parent features (i.e. genes) in your GFF3 like this:

 

ID=sp|A6NHN0|OTOL1_HUMAN;Symbol=OTOL1;

 

And then making that searchable while loading in the gff file by setting --nameAttributes for flatfile-to-json.pl:

 

flatfile-to-json.pl --gff path/to/file.gff3 --trackLabel “Whatever” --nameAttributes “ID,Symbol”

 

Hope this helps,

 

Travis

 

From: Seyed Ahmad Mousavi [mailto:[hidden email]]
Sent: Monday, July 18, 2016 10:20 AM
To: [hidden email]; Hans Vasquez-Gross <[hidden email]>
Subject: Re: [Gmod-ajax] Searching other feature in JBrowse

 

Dear Hans and friends,

 

As you could see in attached picture my sequences in JBrowse start with e.g "sp|A6NHN0|OTOL1_HUMAN."  I wanted to search part of this accession (like otol1 ) in search box, which one of the following way is possible:

 

1- Adding gene symbol to this sequences by another file?

2- Or, Should I change the names of sequences in GFF file (e.g instead of "sp|A6NHN0|OTOL1_HUMAN" > "OTOL1")?

 

I appreciate your helps.

 

Respectfully,

Ahmad

 

On Mon, Jul 18, 2016 at 11:34 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:

Hi friends,

I have installed JBrowse on my server and I added fasta file (contains > 70k scaffolds ) and a GFF file in JBrowse. Also, I run generate-names.pl script in Jbrowse. Which I just could search scaffold or contig names in it.

 

But as you know GFF files has other features like gene symbol, which is not search-able even after running  generate-names.pl.

My question is how can I add other features like gene symbol along with my contigs name?

I appreciate your helps.

Kind regards,

Ahmad

 


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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Re: Searching other feature in JBrowse

Seyed Ahmad Mousavi
Dear Travis,

Your answer was fast and great solution for showing gene symbol in Jbrowse !!

It works properly now.


Thanks,
Ahmad

On Mon, Jul 18, 2016 at 8:52 PM, Saari, Travis <[hidden email]> wrote:

Hi Ahmad,

 

You can do it that way, but another way which preserves your ID’s would be to add a Symbol tag to the parent features (i.e. genes) in your GFF3 like this:

 

ID=sp|A6NHN0|OTOL1_HUMAN;Symbol=OTOL1;

 

And then making that searchable while loading in the gff file by setting --nameAttributes for flatfile-to-json.pl:

 

flatfile-to-json.pl --gff path/to/file.gff3 --trackLabel “Whatever” --nameAttributes “ID,Symbol”

 

Hope this helps,

 

Travis

 

From: Seyed Ahmad Mousavi [mailto:[hidden email]]
Sent: Monday, July 18, 2016 10:20 AM
To: [hidden email]; Hans Vasquez-Gross <[hidden email]>
Subject: Re: [Gmod-ajax] Searching other feature in JBrowse

 

Dear Hans and friends,

 

As you could see in attached picture my sequences in JBrowse start with e.g "sp|A6NHN0|OTOL1_HUMAN."  I wanted to search part of this accession (like otol1 ) in search box, which one of the following way is possible:

 

1- Adding gene symbol to this sequences by another file?

2- Or, Should I change the names of sequences in GFF file (e.g instead of "sp|A6NHN0|OTOL1_HUMAN" > "OTOL1")?

 

I appreciate your helps.

 

Respectfully,

Ahmad

 

On Mon, Jul 18, 2016 at 11:34 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:

Hi friends,

I have installed JBrowse on my server and I added fasta file (contains > 70k scaffolds ) and a GFF file in JBrowse. Also, I run generate-names.pl script in Jbrowse. Which I just could search scaffold or contig names in it.

 

But as you know GFF files has other features like gene symbol, which is not search-able even after running  generate-names.pl.

My question is how can I add other features like gene symbol along with my contigs name?

I appreciate your helps.

Kind regards,

Ahmad

 



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax