[Gmod-ajax] setting up jbrowse with a bacterial reference genome

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[Gmod-ajax] setting up jbrowse with a bacterial reference genome

Heewook Lee
Hi, I got all the components installed and jbrowse is running. I am trying to load ecoli onto jbrowse from NCBI files. I downloaded their gff file and the reference sequence in fasta format. What's the best way to get this set up?

-hl

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Re: setting up jbrowse with a bacterial reference genome

Robert Buels-2
Hi Heewook,

The best thing to do would be to write a little JSON conf file
specifying how you want the tracks to be displayed, then use
bin/biodb-to-json.pl to format them into your data/ directory.

See http://jbrowse.org/code/jbrowse-master/docs/tutorial/ for details.

Let me know if you have any more questions!

Rob


On 02/10/2012 11:54 AM, Heewook Lee wrote:

> Hi, I got all the components installed and jbrowse is running. I am
> trying to load ecoli onto jbrowse from NCBI files. I downloaded their
> gff file and the reference sequence in fasta format. What's the best way
> to get this set up?
>
> -hl
>
>
>
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Re: setting up jbrowse with a bacterial reference genome

Robert Buels-2
In reply to this post by Heewook Lee
Hi Heewook,

The best thing to do would be to write a little JSON conf file
specifying how you want the tracks to be displayed, then use
bin/biodb-to-json.pl to format them into your data/ directory.

See http://jbrowse.org/code/jbrowse-master/docs/tutorial/ for details.

Let me know if you have any more questions!

Rob

On 02/10/2012 11:54 AM, Heewook Lee wrote:
> Hi, I got all the components installed and jbrowse is running. I am
> trying to load ecoli onto jbrowse from NCBI files. I downloaded their
> gff file and the reference sequence in fasta format. What's the best way
> to get this set up?

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Re: setting up jbrowse with a bacterial reference genome

Heewook Lee
I am actually looking at a document: Setting Up the JBrowse Genome Browser that was published in Current Protocols in Bioinformatics in 2010 and there is an example using NCBI gbk file. I tried that but I am getting the following error:

[heewlee@ngs tmp]$ bin/prepare-refseqs.pl --conf docs/examples/config/yeast_genbank.json --refs NC_001133

-------------------- EXCEPTION --------------------
MSG: segment() called in a scalar context but multiple features match.
Either call in a list context or narrow your search using the -types or -class arguments

STACK Bio::DB::SeqFeature::Store::segment /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:1359
STACK toplevel bin/prepare-refseqs.pl:156
-------------------------------------------

Any idea how I can get around this? Thanks

On Fri, Feb 10, 2012 at 12:34 PM, Robert Buels <[hidden email]> wrote:
Hi Heewook,

The best thing to do would be to write a little JSON conf file specifying how you want the tracks to be displayed, then use bin/biodb-to-json.pl to format them into your data/ directory.

See http://jbrowse.org/code/jbrowse-master/docs/tutorial/ for details.

Let me know if you have any more questions!

Rob


On 02/10/2012 11:54 AM, Heewook Lee wrote:
Hi, I got all the components installed and jbrowse is running. I am
trying to load ecoli onto jbrowse from NCBI files. I downloaded their
gff file and the reference sequence in fasta format. What's the best way
to get this set up?


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Re: setting up jbrowse with a bacterial reference genome

Robert Buels-2
Hi Heewook,

Bio::DB::SeqFeature::Store's behavior has changed slightly since that
Current Protocols publication was written.  In the NC_001133.gbk.gff,
just remove the ##sequence-region line that the directions in the
publication told you to alter, and the error should go away.  Sorry for
the inconvenience.

Rob


On 02/10/2012 01:32 PM, Heewook Lee wrote:

> -------------------- EXCEPTION --------------------
> MSG: segment() called in a scalar context but multiple features match.
> Either call in a list context or narrow your search using the -types or
> -class arguments
>
> STACK Bio::DB::SeqFeature::Store::segment
> /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:1359
> STACK toplevel bin/prepare-refseqs.pl:156 <http://prepare-refseqs.pl:156>
> -------------------------------------------
>
> Any idea how I can get around this? Thanks

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Re: setting up jbrowse with a bacterial reference genome

Heewook Lee
Thanks. It works great! 

I have one more question though. So now I have set up the jbrowse (using gbk2gff then biodb-to-json.pl with a config file similar to yeast configuration file you provide with the tarball) and now I want to add a track for displaying point mutations. I have already prepared the point mutations in a gff3 format so each point mutation in gff file is as :

ecoli SNP 9010 9010 . . . ID=ecoli_9010;Name=ecoli_9010;Reference_Base=C;Consensus=C;Modified_Call=T;snp_type=N-Syn

since i have these point mutations in a separate file, I used bin/flatfile-to-json.pl :

$bin/flatfile-to-json.pl --gff pointMutations.gff --tracklabel SNP --key SNP

After this, when I refresh the jbrowse, I can see that new track, SNP has been added but the problem is it's not being rendered on the browser. When I zoom out enough I can see a histogram for the track but when i zoom in, I see nothing. What would I need to do to display SNPs correctly? Thanks!



On Wed, Feb 15, 2012 at 12:14 PM, Robert Buels <[hidden email]> wrote:
Hi Heewook,

Bio::DB::SeqFeature::Store's behavior has changed slightly since that Current Protocols publication was written.  In the NC_001133.gbk.gff, just remove the ##sequence-region line that the directions in the publication told you to alter, and the error should go away.  Sorry for the inconvenience.

Rob



On 02/10/2012 01:32 PM, Heewook Lee wrote:
-------------------- EXCEPTION --------------------
MSG: segment() called in a scalar context but multiple features match.
Either call in a list context or narrow your search using the -types or
-class arguments

STACK Bio::DB::SeqFeature::Store::segment
/usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:1359
STACK toplevel bin/prepare-refseqs.pl:156 <http://prepare-refseqs.pl:156>

-------------------------------------------

Any idea how I can get around this? Thanks


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Re: setting up jbrowse with a bacterial reference genome

Robert Buels-2
Hi Heewook,

Do you have the browser online anywhere that I can look at it?  That
would help me diagnose what's going on.

If you can't put it online, could you email me the
data/tracks/*/SNP/trackData.json and data/trackInfo.js files so I can
look at them?

Rob


On 02/25/2012 01:44 AM, Heewook Lee wrote:

> Thanks. It works great!
>
> I have one more question though. So now I have set up the jbrowse (using
> gbk2gff then biodb-to-json.pl <http://biodb-to-json.pl> with a config
> file similar to yeast configuration file you provide with the tarball)
> and now I want to add a track for displaying point mutations. I have
> already prepared the point mutations in a gff3 format so each point
> mutation in gff file is as :
>
> ecoliSNP90109010...ID=ecoli_9010;Name=ecoli_9010;Reference_Base=C;Consensus=C;Modified_Call=T;snp_type=N-Syn
>
> since i have these point mutations in a separate file, I
> used bin/flatfile-to-json.pl <http://flatfile-to-json.pl> :
>
> $bin/flatfile-to-json.pl <http://flatfile-to-json.pl> --gff
> pointMutations.gff --tracklabel SNP --key SNP
>
> After this, when I refresh the jbrowse, I can see that new track, SNP
> has been added but the problem is it's not being rendered on the
> browser. When I zoom out enough I can see a histogram for the track but
> when i zoom in, I see nothing. What would I need to do to display SNPs
> correctly? Thanks!
>
>
>
> On Wed, Feb 15, 2012 at 12:14 PM, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Heewook,
>
>     Bio::DB::SeqFeature::Store's behavior has changed slightly since
>     that Current Protocols publication was written.  In the
>     NC_001133.gbk.gff, just remove the ##sequence-region line that the
>     directions in the publication told you to alter, and the error
>     should go away.  Sorry for the inconvenience.
>
>     Rob
>
>
>
>     On 02/10/2012 01:32 PM, Heewook Lee wrote:
>
>         -------------------- EXCEPTION --------------------
>         MSG: segment() called in a scalar context but multiple features
>         match.
>         Either call in a list context or narrow your search using the
>         -types or
>         -class arguments
>
>         STACK Bio::DB::SeqFeature::Store::__segment
>         /usr/local/share/perl5/Bio/DB/__SeqFeature/Store.pm:1359
>         STACK toplevel bin/prepare-refseqs.pl:156
>         <http://prepare-refseqs.pl:156> <<a href="http://prepare-refseqs.pl:156__">http://prepare-refseqs.pl:156__>
>
>         ------------------------------__-------------
>
>         Any idea how I can get around this? Thanks
>
>


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Re: setting up jbrowse with a bacterial reference genome

Heewook Lee
Rob,

Actually i got this solved somehow.. instead of adding single track at a time with the flatfile script, I tured to biodb-to-json.pl. Anyhow, I have one more question:

I have noticed all entries in gff when it's added to jbrowse via biodb-to-json.pl, start index  always gets offset by 1. For example, if you have an entry in gff file and start and end is 1000 2000, when it's added on jbrowse, it will display as "start: 999, end: 2000. Why does this happen and are you aware of this? Thanks!

On Mon, Feb 27, 2012 at 11:29 AM, Robert Buels <[hidden email]> wrote:
Hi Heewook,

Do you have the browser online anywhere that I can look at it?  That would help me diagnose what's going on.

If you can't put it online, could you email me the data/tracks/*/SNP/trackData.json and data/trackInfo.js files so I can look at them?

Rob



On 02/25/2012 01:44 AM, Heewook Lee wrote:
Thanks. It works great!

I have one more question though. So now I have set up the jbrowse (using
gbk2gff then biodb-to-json.pl <http://biodb-to-json.pl> with a config

file similar to yeast configuration file you provide with the tarball)
and now I want to add a track for displaying point mutations. I have
already prepared the point mutations in a gff3 format so each point
mutation in gff file is as :

ecoliSNP90109010...ID=ecoli_9010;Name=ecoli_9010;Reference_Base=C;Consensus=C;Modified_Call=T;snp_type=N-Syn


since i have these point mutations in a separate file, I
used bin/flatfile-to-json.pl <http://flatfile-to-json.pl> :

$bin/flatfile-to-json.pl <http://flatfile-to-json.pl> --gff

pointMutations.gff --tracklabel SNP --key SNP

After this, when I refresh the jbrowse, I can see that new track, SNP
has been added but the problem is it's not being rendered on the
browser. When I zoom out enough I can see a histogram for the track but
when i zoom in, I see nothing. What would I need to do to display SNPs
correctly? Thanks!



On Wed, Feb 15, 2012 at 12:14 PM, Robert Buels <[hidden email]
<mailto:[hidden email]>> wrote:

   Hi Heewook,

   Bio::DB::SeqFeature::Store's behavior has changed slightly since
   that Current Protocols publication was written.  In the
   NC_001133.gbk.gff, just remove the ##sequence-region line that the
   directions in the publication told you to alter, and the error
   should go away.  Sorry for the inconvenience.

   Rob



   On 02/10/2012 01:32 PM, Heewook Lee wrote:

       -------------------- EXCEPTION --------------------
       MSG: segment() called in a scalar context but multiple features
       match.
       Either call in a list context or narrow your search using the
       -types or
       -class arguments

       STACK Bio::DB::SeqFeature::Store::__segment
       /usr/local/share/perl5/Bio/DB/__SeqFeature/Store.pm:1359
       STACK toplevel bin/prepare-refseqs.pl:156
       <http://prepare-refseqs.pl:156> <http://prepare-refseqs.pl:156__>

       ------------------------------__-------------


       Any idea how I can get around this? Thanks





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Re: setting up jbrowse with a bacterial reference genome

Robert Buels-2
Hi Heewook,

I'll take a look.  Could you add this to the JBrowse issue tracker at
https://github.com/GMOD/jbrowse/issues?

Rob

On 02/27/2012 01:17 PM, Heewook Lee wrote:
> I have noticed all entries in gff when it's added to jbrowse via
> biodb-to-json.pl <http://biodb-to-json.pl/>, start index  always
> gets offset by 1. For example, if you have an entry in gff file and
> start and end is 1000 2000, when it's added on jbrowse, it will display
> as "start: 999, end: 2000. Why does this happen and are you aware of
> this? Thanks!

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Re: setting up jbrowse with a bacterial reference genome

Heewook Lee
Done!

On Tue, Feb 28, 2012 at 1:52 PM, Robert Buels <[hidden email]> wrote:
Hi Heewook,

I'll take a look.  Could you add this to the JBrowse issue tracker at
https://github.com/GMOD/jbrowse/issues?

Rob


On 02/27/2012 01:17 PM, Heewook Lee wrote:
I have noticed all entries in gff when it's added to jbrowse via
biodb-to-json.pl <http://biodb-to-json.pl/>, start index  always

gets offset by 1. For example, if you have an entry in gff file and
start and end is 1000 2000, when it's added on jbrowse, it will display
as "start: 999, end: 2000. Why does this happen and are you aware of
this? Thanks!


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Re: setting up jbrowse with a bacterial reference genome

Robert Buels-2
Fixed in master, issue URL: https://github.com/gmod/jbrowse/issues/73

On 02/28/2012 02:11 PM, Heewook Lee wrote:

> Done!
>
> On Tue, Feb 28, 2012 at 1:52 PM, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Heewook,
>
>     I'll take a look.  Could you add this to the JBrowse issue tracker at
>     https://github.com/GMOD/__jbrowse/issues
>     <https://github.com/GMOD/jbrowse/issues>?
>
>     Rob
>
>
>     On 02/27/2012 01:17 PM, Heewook Lee wrote:
>
>         I have noticed all entries in gff when it's added to jbrowse via
>         biodb-to-json.pl <http://biodb-to-json.pl>
>         <http://biodb-to-json.pl/>, start index  always
>
>         gets offset by 1. For example, if you have an entry in gff file and
>         start and end is 1000 2000, when it's added on jbrowse, it will
>         display
>         as "start: 999, end: 2000. Why does this happen and are you aware of
>         this? Thanks!
>
>


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Re: setting up jbrowse with a bacterial reference genome

Heewook Lee
Thank you so much! just surprised this went undetected till now. :)

-hl

On Wed, Feb 29, 2012 at 3:06 PM, Robert Buels <[hidden email]> wrote:
Fixed in master, issue URL: https://github.com/gmod/jbrowse/issues/73


On 02/28/2012 02:11 PM, Heewook Lee wrote:
Done!

On Tue, Feb 28, 2012 at 1:52 PM, Robert Buels <[hidden email]
<mailto:[hidden email]>> wrote:

   Hi Heewook,

   I'll take a look.  Could you add this to the JBrowse issue tracker at
   https://github.com/GMOD/__jbrowse/issues
   <https://github.com/GMOD/jbrowse/issues>?


   Rob


   On 02/27/2012 01:17 PM, Heewook Lee wrote:

       I have noticed all entries in gff when it's added to jbrowse via
       biodb-to-json.pl <http://biodb-to-json.pl>
       <http://biodb-to-json.pl/>, start index  always

       gets offset by 1. For example, if you have an entry in gff file and
       start and end is 1000 2000, when it's added on jbrowse, it will
       display
       as "start: 999, end: 2000. Why does this happen and are you aware of
       this? Thanks!





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Re: setting up jbrowse with a bacterial reference genome

Karsten Hokamp
In reply to this post by Robert Buels-2
Hi,

I'm not sure this was a bug. In a previous discussion it was noted
that JBrowse was 0-based, see from message 5 onwards in this thread:
http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-td998491.html

However, there was mentioning of changing this to 1-based for the user
interface and I suppose this is done now.

Thanks,

    Karsten


On Wed, Feb 29, 2012 at 8:06 PM, Robert Buels <[hidden email]> wrote:

> Fixed in master, issue URL: https://github.com/gmod/jbrowse/issues/73
>
> On 02/28/2012 02:11 PM, Heewook Lee wrote:
>> Done!
>>
>> On Tue, Feb 28, 2012 at 1:52 PM, Robert Buels <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>     Hi Heewook,
>>
>>     I'll take a look.  Could you add this to the JBrowse issue tracker at
>>     https://github.com/GMOD/__jbrowse/issues
>>     <https://github.com/GMOD/jbrowse/issues>?
>>
>>     Rob
>>
>>
>>     On 02/27/2012 01:17 PM, Heewook Lee wrote:
>>
>>         I have noticed all entries in gff when it's added to jbrowse via
>>         biodb-to-json.pl <http://biodb-to-json.pl>
>>         <http://biodb-to-json.pl/>, start index  always
>>
>>         gets offset by 1. For example, if you have an entry in gff file and
>>         start and end is 1000 2000, when it's added on jbrowse, it will
>>         display
>>         as "start: 999, end: 2000. Why does this happen and are you aware of
>>         this? Thanks!
>>
>>
>
>
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Re: setting up jbrowse with a bacterial reference genome

Robert Buels-2
Ah, I'd missed this up to now.  Yes, it seems it's all 0-based
half-open.  I'll revert that commit.  Thanks a lot for pointing that out
Karsten.

I'll add a ticket to convert everything shown to the user to be 1-based
closed coordinates, because that's what people expect to see.

Rob

On 02/29/2012 05:21 PM, Karsten Hokamp wrote:

> Hi,
>
> I'm not sure this was a bug. In a previous discussion it was noted
> that JBrowse was 0-based, see from message 5 onwards in this thread:
> http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-td998491.html
>
> However, there was mentioning of changing this to 1-based for the user
> interface and I suppose this is done now.
>
> Thanks,
>
>      Karsten
>
>
> On Wed, Feb 29, 2012 at 8:06 PM, Robert Buels<[hidden email]>  wrote:
>> Fixed in master, issue URL: https://github.com/gmod/jbrowse/issues/73
>>
>> On 02/28/2012 02:11 PM, Heewook Lee wrote:
>>> Done!
>>>
>>> On Tue, Feb 28, 2012 at 1:52 PM, Robert Buels<[hidden email]
>>> <mailto:[hidden email]>>  wrote:
>>>
>>>      Hi Heewook,
>>>
>>>      I'll take a look.  Could you add this to the JBrowse issue tracker at
>>>      https://github.com/GMOD/__jbrowse/issues
>>>      <https://github.com/GMOD/jbrowse/issues>?
>>>
>>>      Rob
>>>
>>>
>>>      On 02/27/2012 01:17 PM, Heewook Lee wrote:
>>>
>>>          I have noticed all entries in gff when it's added to jbrowse via
>>>          biodb-to-json.pl<http://biodb-to-json.pl>
>>>          <http://biodb-to-json.pl/>, start index  always
>>>
>>>          gets offset by 1. For example, if you have an entry in gff file and
>>>          start and end is 1000 2000, when it's added on jbrowse, it will
>>>          display
>>>          as "start: 999, end: 2000. Why does this happen and are you aware of
>>>          this? Thanks!
>>>
>>>
>>
>>
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Re: setting up jbrowse with a bacterial reference genome

Heewook Lee
In reply to this post by Karsten Hokamp
0-based half-open explains but then the bug is not the interval but rendering/drawing of elements because if you have an element that is single-base event such as SNP, the drawing will take up 2bp rather than 1bp. 

For example, SNP is at 1,000 in genbank file(which is 1-based), then when you add this to jbrowse, this will be displayed as (Start: 999, end:1000). Since the end interval is open interval 1000 should not be included in the drawing, however, if you zoom in all the way you can surely tell that jbrowse will render this event as 2bp.

Right now, i am using triangle from genome.css to display a SNP and when you zoom all the way in(1bp-resolution), the triangle will turn into isosceles trapezoid because it takes up 2bp. 

-hl

On Wed, Feb 29, 2012 at 5:21 PM, Karsten Hokamp <[hidden email]> wrote:
Hi,

I'm not sure this was a bug. In a previous discussion it was noted
that JBrowse was 0-based, see from message 5 onwards in this thread:
http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-td998491.html

However, there was mentioning of changing this to 1-based for the user
interface and I suppose this is done now.

Thanks,

   Karsten


On Wed, Feb 29, 2012 at 8:06 PM, Robert Buels <[hidden email]> wrote:
> Fixed in master, issue URL: https://github.com/gmod/jbrowse/issues/73
>
> On 02/28/2012 02:11 PM, Heewook Lee wrote:
>> Done!
>>
>> On Tue, Feb 28, 2012 at 1:52 PM, Robert Buels <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>     Hi Heewook,
>>
>>     I'll take a look.  Could you add this to the JBrowse issue tracker at
>>     https://github.com/GMOD/__jbrowse/issues
>>     <https://github.com/GMOD/jbrowse/issues>?
>>
>>     Rob
>>
>>
>>     On 02/27/2012 01:17 PM, Heewook Lee wrote:
>>
>>         I have noticed all entries in gff when it's added to jbrowse via
>>         biodb-to-json.pl <http://biodb-to-json.pl>
>>         <http://biodb-to-json.pl/>, start index  always
>>
>>         gets offset by 1. For example, if you have an entry in gff file and
>>         start and end is 1000 2000, when it's added on jbrowse, it will
>>         display
>>         as "start: 999, end: 2000. Why does this happen and are you aware of
>>         this? Thanks!
>>
>>
>
>
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[Gmod-ajax] refSeqs & trackInfo

Mariette
Hi everyone,

I have hard time to understand how is managed the refSeqs & the
trackInfo params when building a jbrowse object.
I'd like to set the path to the js but it's not working. There is any
way to provide the right path to the js file other than
including it inside the html page ?

thanks for your reply,
Jerome

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Re: refSeqs & trackInfo

Robert Buels-2
Hi Jerome,

In JBrowse 1.2.1, the data/refSeqs.js and data/trackInfo.js must be
included in the index.html.

In the coming release, however, this will be passable as a parameter to
the JBrowse object.

Rob

On 03/01/2012 11:28 AM, Mariette wrote:

> Hi everyone,
>
> I have hard time to understand how is managed the refSeqs&  the
> trackInfo params when building a jbrowse object.
> I'd like to set the path to the js but it's not working. There is any
> way to provide the right path to the js file other than
> including it inside the html page ?
>
> thanks for your reply,
> Jerome
>
> ------------------------------------------------------------------------------
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> also focuses on allowing computing to be delivered as a service.
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Re: refSeqs & trackInfo

Mariette

Thanks Rob for your answer!

When do you think the new vesion will be released ?
(It's just to know if I have to implement something to make jbrowse work
with the current version)

Jerome



Le 01/03/2012 18:12, Robert Buels a écrit :

> Hi Jerome,
>
> In JBrowse 1.2.1, the data/refSeqs.js and data/trackInfo.js must be
> included in the index.html.
>
> In the coming release, however, this will be passable as a parameter
> to the JBrowse object.
>
> Rob
>
> On 03/01/2012 11:28 AM, Mariette wrote:
>> Hi everyone,
>>
>> I have hard time to understand how is managed the refSeqs&  the
>> trackInfo params when building a jbrowse object.
>> I'd like to set the path to the js but it's not working. There is any
>> way to provide the right path to the js file other than
>> including it inside the html page ?
>>
>> thanks for your reply,
>> Jerome
>>
>> ------------------------------------------------------------------------------
>>
>> Virtualization&  Cloud Management Using Capacity Planning
>> Cloud computing makes use of virtualization - but cloud computing
>> also focuses on allowing computing to be delivered as a service.
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>


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Re: setting up jbrowse with a bacterial reference genome

Robert Buels-2
In reply to this post by Heewook Lee
On 02/29/2012 06:45 PM, Heewook Lee wrote:
> Right now, i am using triangle from genome.css to display a SNP and when
> you zoom all the way in(1bp-resolution), the triangle will turn
> into isosceles trapezoid because it takes up 2bp.

I looked into this 2-base issue, and I think it's caused by the fact
that the triangle glyph is implemented with a hackish CSS trick
involving border widths, and this turns out not to work very well for
single-base features.  Try using a different glyph for your SNPs.
"dblhelix" might be an OK one.

As for the interbase (i.e. 0-based half-open) coordinates issue, I have
a ticket open to show everything in the user interface as 1-based
coordinates.  It's https://github.com/GMOD/jbrowse/issues/74.  I'm
actually working on that right now, since it's both important and a
relatively easy fix.

Rob

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Re: setting up jbrowse with a bacterial reference genome

Heewook Lee
Thanks!

-hl

On Fri, Mar 2, 2012 at 10:12 AM, Robert Buels <[hidden email]> wrote:
On 02/29/2012 06:45 PM, Heewook Lee wrote:
Right now, i am using triangle from genome.css to display a SNP and when
you zoom all the way in(1bp-resolution), the triangle will turn
into isosceles trapezoid because it takes up 2bp.

I looked into this 2-base issue, and I think it's caused by the fact that the triangle glyph is implemented with a hackish CSS trick involving border widths, and this turns out not to work very well for single-base features.  Try using a different glyph for your SNPs. "dblhelix" might be an OK one.

As for the interbase (i.e. 0-based half-open) coordinates issue, I have a ticket open to show everything in the user interface as 1-based coordinates.  It's https://github.com/GMOD/jbrowse/issues/74.  I'm actually working on that right now, since it's both important and a relatively easy fix.

Rob


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