BigBed in gbrowse

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BigBed in gbrowse

Chandan Kumar Singh
Hi

Has anybody tried visualizing junctions.bed (output from tophat)
using Gbrowse2? I am particularly interested in visualizing BigBed
format (converted from junctions.bed). BTW, converting the BED format
to GFF3 and then using gbrowse works.

Thanks
Chandan

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Re: BigBed in gbrowse

Chandan Kumar Singh
Hi

Has anyone been using BigBed for data display in gbrowse?

Thanks
Chandan


On Thu, Jun 23, 2011 at 12:01 PM, CHANDAN SINGH
<[hidden email]> wrote:

> Hi
>
> Has anybody tried visualizing junctions.bed (output from tophat)
> using Gbrowse2? I am particularly interested in visualizing BigBed
> format (converted from junctions.bed). BTW, converting the BED format
> to GFF3 and then using gbrowse works.
>
> Thanks
> Chandan
>

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense..
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Re: BigBed in gbrowse

Timothy Parnell
Hi Chandan,

I have used BigBed once, but only to visualize simple sequence alignments
that were already in BED format. The alignments weren't gapped, so I
didn't have to work with multiple blocks. I understand that it supports
multiple blocks, but treats them as mRNA->UTR,CDS convenient for the
transcript or gene glyphs. I haven't used it specifically with a
junctions.bed from tophat, but will have to remember to try that next time.

GBrowse won't handle BigBed uploads or even remote URLs, so you'll have to
write it in the conf file yourself. I just used the segments glyph for my
purposes, but you can also use the transcript or wiggle_whisker glyphs as
appropriate.

Tim

On 6/24/11 12:42 PM, "CHANDAN SINGH" <[hidden email]> wrote:

>Hi
>
>Has anyone been using BigBed for data display in gbrowse?
>
>Thanks
>Chandan
>
>
>On Thu, Jun 23, 2011 at 12:01 PM, CHANDAN SINGH
><[hidden email]> wrote:
>> Hi
>>
>> Has anybody tried visualizing junctions.bed (output from tophat)
>> using Gbrowse2? I am particularly interested in visualizing BigBed
>> format (converted from junctions.bed). BTW, converting the BED format
>> to GFF3 and then using gbrowse works.
>>
>> Thanks
>> Chandan
>>
>
>--------------------------------------------------------------------------
>----
>All the data continuously generated in your IT infrastructure contains a
>definitive record of customers, application performance, security
>threats, fraudulent activity and more. Splunk takes this data and makes
>sense of it. Business sense. IT sense. Common sense..
>http://p.sf.net/sfu/splunk-d2d-c1
>_______________________________________________
>Gmod-gbrowse mailing list
>[hidden email]
>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense..
http://p.sf.net/sfu/splunk-d2d-c1
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Re: BigBed in gbrowse

Chandan Kumar Singh
Hi Timothy

I tried many configuration changes but was unable to get anything from
BigBed file. There is no error logged but the track is always empty.

I can upload the bigbed file on UCSC genome browser and get
appropriate output. I can also use Bio::Graphics directly and get
appropriate images from the BigBed file.

I will be very thankful if you or anybody else, with sufficient
experience with Gbrowse, can confirm if there is a bug with Bigbed
handling.

Thanks
Chandan


On Sat, Jun 25, 2011 at 3:56 AM, Timothy Parnell
<[hidden email]> wrote:

> Hi Chandan,
>
> I have used BigBed once, but only to visualize simple sequence alignments
> that were already in BED format. The alignments weren't gapped, so I
> didn't have to work with multiple blocks. I understand that it supports
> multiple blocks, but treats them as mRNA->UTR,CDS convenient for the
> transcript or gene glyphs. I haven't used it specifically with a
> junctions.bed from tophat, but will have to remember to try that next time.
>
> GBrowse won't handle BigBed uploads or even remote URLs, so you'll have to
> write it in the conf file yourself. I just used the segments glyph for my
> purposes, but you can also use the transcript or wiggle_whisker glyphs as
> appropriate.
>
> Tim
>
> On 6/24/11 12:42 PM, "CHANDAN SINGH" <[hidden email]> wrote:
>
>>Hi
>>
>>Has anyone been using BigBed for data display in gbrowse?
>>
>>Thanks
>>Chandan
>>
>>
>>On Thu, Jun 23, 2011 at 12:01 PM, CHANDAN SINGH
>><[hidden email]> wrote:
>>> Hi
>>>
>>> Has anybody tried visualizing junctions.bed (output from tophat)
>>> using Gbrowse2? I am particularly interested in visualizing BigBed
>>> format (converted from junctions.bed). BTW, converting the BED format
>>> to GFF3 and then using gbrowse works.
>>>
>>> Thanks
>>> Chandan
>>>
>>
>>--------------------------------------------------------------------------
>>----
>>All the data continuously generated in your IT infrastructure contains a
>>definitive record of customers, application performance, security
>>threats, fraudulent activity and more. Splunk takes this data and makes
>>sense of it. Business sense. IT sense. Common sense..
>>http://p.sf.net/sfu/splunk-d2d-c1
>>_______________________________________________
>>Gmod-gbrowse mailing list
>>[hidden email]
>>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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Re: BigBed in gbrowse

Timothy Parnell
Hi Chandan,

Sorry to hear it's not working for you. This is the conf I used
successfully with visualizing next generation sequence alignments in BED
format using GBrowse 2.37 and Bio-BigFile 1.06

[8833p_bed_db:database]
db_adaptor    = Bio::DB::BigBed
db_args       = -bigbed /Library/WebServer/Bam_data/8833p_reads.bb

[8833p_bed_reads]
database     = 8833p_bed_db
feature      = region
glyph        = generic
fgcolor      = blue
bgcolor      = sub {
   my $f = shift;
   return $f->strand == 1 ? 'blue' : 'red';
   }
height       = 3
stranded     = 1

The fasta option to the db_args is helpful, but not required. Use the
region feature for visualizing segments with the generic or segments
glyphs, or use the summary feature for use with the wiggle_xyplot or
wiggle_whiskers glyphs.

Hope you can glean something useful from this. Otherwise, have you tried
all the usual troubleshooting tips (track caching, invalid characters in
the conf, permissions, etc).

Tim



On 6/27/11 3:25 AM, "CHANDAN SINGH" <[hidden email]> wrote:

>Hi Timothy
>
>I tried many configuration changes but was unable to get anything from
>BigBed file. There is no error logged but the track is always empty.
>
>I can upload the bigbed file on UCSC genome browser and get
>appropriate output. I can also use Bio::Graphics directly and get
>appropriate images from the BigBed file.
>
>I will be very thankful if you or anybody else, with sufficient
>experience with Gbrowse, can confirm if there is a bug with Bigbed
>handling.
>
>Thanks
>Chandan
>
>
>On Sat, Jun 25, 2011 at 3:56 AM, Timothy Parnell
><[hidden email]> wrote:
>> Hi Chandan,
>>
>> I have used BigBed once, but only to visualize simple sequence
>>alignments
>> that were already in BED format. The alignments weren't gapped, so I
>> didn't have to work with multiple blocks. I understand that it supports
>> multiple blocks, but treats them as mRNA->UTR,CDS convenient for the
>> transcript or gene glyphs. I haven't used it specifically with a
>> junctions.bed from tophat, but will have to remember to try that next
>>time.
>>
>> GBrowse won't handle BigBed uploads or even remote URLs, so you'll have
>>to
>> write it in the conf file yourself. I just used the segments glyph for
>>my
>> purposes, but you can also use the transcript or wiggle_whisker glyphs
>>as
>> appropriate.
>>
>> Tim
>>
>> On 6/24/11 12:42 PM, "CHANDAN SINGH" <[hidden email]> wrote:
>>
>>>Hi
>>>
>>>Has anyone been using BigBed for data display in gbrowse?
>>>
>>>Thanks
>>>Chandan
>>>
>>>
>>>On Thu, Jun 23, 2011 at 12:01 PM, CHANDAN SINGH
>>><[hidden email]> wrote:
>>>> Hi
>>>>
>>>> Has anybody tried visualizing junctions.bed (output from tophat)
>>>> using Gbrowse2? I am particularly interested in visualizing BigBed
>>>> format (converted from junctions.bed). BTW, converting the BED format
>>>> to GFF3 and then using gbrowse works.
>>>>
>>>> Thanks
>>>> Chandan
>>>>
>>>
>>>------------------------------------------------------------------------
>>>--
>>>----
>>>All the data continuously generated in your IT infrastructure contains a
>>>definitive record of customers, application performance, security
>>>threats, fraudulent activity and more. Splunk takes this data and makes
>>>sense of it. Business sense. IT sense. Common sense..
>>>http://p.sf.net/sfu/splunk-d2d-c1
>>>_______________________________________________
>>>Gmod-gbrowse mailing list
>>>[hidden email]
>>>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>


------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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Re: BigBed in gbrowse

Lincoln Stein
In reply to this post by Chandan Kumar Singh
BigBed display should work by directly editing the config file, but uploads won't recognize them yet. If you could send me an example junctions.bed file, I can write in the support and make sure that the file displays correctly.

Lincoln

On Mon, Jun 27, 2011 at 5:25 AM, CHANDAN SINGH <[hidden email]> wrote:
Hi Timothy

I tried many configuration changes but was unable to get anything from
BigBed file. There is no error logged but the track is always empty.

I can upload the bigbed file on UCSC genome browser and get
appropriate output. I can also use Bio::Graphics directly and get
appropriate images from the BigBed file.

I will be very thankful if you or anybody else, with sufficient
experience with Gbrowse, can confirm if there is a bug with Bigbed
handling.

Thanks
Chandan


On Sat, Jun 25, 2011 at 3:56 AM, Timothy Parnell
<[hidden email]> wrote:
> Hi Chandan,
>
> I have used BigBed once, but only to visualize simple sequence alignments
> that were already in BED format. The alignments weren't gapped, so I
> didn't have to work with multiple blocks. I understand that it supports
> multiple blocks, but treats them as mRNA->UTR,CDS convenient for the
> transcript or gene glyphs. I haven't used it specifically with a
> junctions.bed from tophat, but will have to remember to try that next time.
>
> GBrowse won't handle BigBed uploads or even remote URLs, so you'll have to
> write it in the conf file yourself. I just used the segments glyph for my
> purposes, but you can also use the transcript or wiggle_whisker glyphs as
> appropriate.
>
> Tim
>
> On 6/24/11 12:42 PM, "CHANDAN SINGH" <[hidden email]> wrote:
>
>>Hi
>>
>>Has anyone been using BigBed for data display in gbrowse?
>>
>>Thanks
>>Chandan
>>
>>
>>On Thu, Jun 23, 2011 at 12:01 PM, CHANDAN SINGH
>><[hidden email]> wrote:
>>> Hi
>>>
>>> Has anybody tried visualizing junctions.bed (output from tophat)
>>> using Gbrowse2? I am particularly interested in visualizing BigBed
>>> format (converted from junctions.bed). BTW, converting the BED format
>>> to GFF3 and then using gbrowse works.
>>>
>>> Thanks
>>> Chandan
>>>
>>
>>--------------------------------------------------------------------------
>>----
>>All the data continuously generated in your IT infrastructure contains a
>>definitive record of customers, application performance, security
>>threats, fraudulent activity and more. Splunk takes this data and makes
>>sense of it. Business sense. IT sense. Common sense..
>>http://p.sf.net/sfu/splunk-d2d-c1
>>_______________________________________________
>>Gmod-gbrowse mailing list
>>[hidden email]
>>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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Re: BigBed in gbrowse

Chandan Kumar Singh
Hi Tim , Lincoln

I'm using Gbrowse 2.38 and BigFile 1.06.  I tried using the conf
suggested by Tim but "feature = region" gives an error (shown below)
while OTOH "feature = mRNA" does not give any output/error.

Error log
-------------
RenderPanels error: Can't call method "next_seq" without a package or
object reference at
/usr/local/lib/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 1657.,
referer: http://localhost/cgi-bin/gb2/gbrowse/data2/

I've attached the bed file so that you can try if possible. To
confess, I  myself,  did not give enough time into it after reading
your mails because I am hard pressed to demonstrate whatever worked
with gbrowse but will surely put more effort after 3 days.

Thanks
Chandan



Thanks
Chandan





On Mon, Jun 27, 2011 at 11:59 PM, Lincoln Stein <[hidden email]> wrote:

> BigBed display should work by directly editing the config file, but uploads
> won't recognize them yet. If you could send me an example junctions.bed
> file, I can write in the support and make sure that the file displays
> correctly.
> Lincoln
>
> On Mon, Jun 27, 2011 at 5:25 AM, CHANDAN SINGH <[hidden email]>
> wrote:
>>
>> Hi Timothy
>>
>> I tried many configuration changes but was unable to get anything from
>> BigBed file. There is no error logged but the track is always empty.
>>
>> I can upload the bigbed file on UCSC genome browser and get
>> appropriate output. I can also use Bio::Graphics directly and get
>> appropriate images from the BigBed file.
>>
>> I will be very thankful if you or anybody else, with sufficient
>> experience with Gbrowse, can confirm if there is a bug with Bigbed
>> handling.
>>
>> Thanks
>> Chandan
>>
>>
>> On Sat, Jun 25, 2011 at 3:56 AM, Timothy Parnell
>> <[hidden email]> wrote:
>> > Hi Chandan,
>> >
>> > I have used BigBed once, but only to visualize simple sequence
>> > alignments
>> > that were already in BED format. The alignments weren't gapped, so I
>> > didn't have to work with multiple blocks. I understand that it supports
>> > multiple blocks, but treats them as mRNA->UTR,CDS convenient for the
>> > transcript or gene glyphs. I haven't used it specifically with a
>> > junctions.bed from tophat, but will have to remember to try that next
>> > time.
>> >
>> > GBrowse won't handle BigBed uploads or even remote URLs, so you'll have
>> > to
>> > write it in the conf file yourself. I just used the segments glyph for
>> > my
>> > purposes, but you can also use the transcript or wiggle_whisker glyphs
>> > as
>> > appropriate.
>> >
>> > Tim
>> >
>> > On 6/24/11 12:42 PM, "CHANDAN SINGH" <[hidden email]> wrote:
>> >
>> >>Hi
>> >>
>> >>Has anyone been using BigBed for data display in gbrowse?
>> >>
>> >>Thanks
>> >>Chandan
>> >>
>> >>
>> >>On Thu, Jun 23, 2011 at 12:01 PM, CHANDAN SINGH
>> >><[hidden email]> wrote:
>> >>> Hi
>> >>>
>> >>> Has anybody tried visualizing junctions.bed (output from tophat)
>> >>> using Gbrowse2? I am particularly interested in visualizing BigBed
>> >>> format (converted from junctions.bed). BTW, converting the BED format
>> >>> to GFF3 and then using gbrowse works.
>> >>>
>> >>> Thanks
>> >>> Chandan
>> >>>
>> >>
>>
>> >> >>--------------------------------------------------------------------------
>> >>----
>> >>All the data continuously generated in your IT infrastructure contains a
>> >>definitive record of customers, application performance, security
>> >>threats, fraudulent activity and more. Splunk takes this data and makes
>> >>sense of it. Business sense. IT sense. Common sense..
>> >>http://p.sf.net/sfu/splunk-d2d-c1
>> >>_______________________________________________
>> >>Gmod-gbrowse mailing list
>> >>[hidden email]
>> >>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
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Re: BigBed in gbrowse

Naoki Amano
Hi,

I also have failed to display BigBed ( and BigWig) file.  However when I
changed the order of database in conf file,
BigBed files was shown in GBrowse.

-Fail Case

[GENREAL]
description = human
database   = annotaions     <-------- Bio::DB::SeqFeature::Store
database  =  testbed         <---------Bio::DB::BigBed

--Successful case
[GENREAL]
description = human
database  =  testbed         <---------Bio::DB::BigBed
database   = annotaions     <-------- Bio::DB::SeqFeature::Store

In my case,  when the order of database for bigbed was last,  the result was
error.

I don't know your case was same as my case, however if your order of BigBed
database was last,
it is worth to change the order of it.

Regards,

Naoki Amano



--
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Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
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Why? It contains a definitive record of application performance, security
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http://p.sf.net/sfu/splunk-d2d-c2
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Re: BigBed in gbrowse

Fields, Christopher J
You shouldn't need the SF::Store database at all, just the BigBed.

chris

On Jul 2, 2011, at 6:45 AM, Naoki Amano wrote:

> Hi,
>
> I also have failed to display BigBed ( and BigWig) file.  However when I
> changed the order of database in conf file,
> BigBed files was shown in GBrowse.
>
> -Fail Case
>
> [GENREAL]
> description = human
> database   = annotaions     <-------- Bio::DB::SeqFeature::Store
> database  =  testbed         <---------Bio::DB::BigBed
>
> --Successful case
> [GENREAL]
> description = human
> database  =  testbed         <---------Bio::DB::BigBed
> database   = annotaions     <-------- Bio::DB::SeqFeature::Store
>
> In my case,  when the order of database for bigbed was last,  the result was
> error.
>
> I don't know your case was same as my case, however if your order of BigBed
> database was last,
> it is worth to change the order of it.
>
> Regards,
>
> Naoki Amano
>
>
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/BigBed-in-gbrowse-tp4516492p4544542.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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Re: BigBed in gbrowse

Chandan Kumar Singh
In reply to this post by Naoki Amano
Hi Naoki

You don't need to give multiple databases in the GENERAL section. I
suppose the last will be the one to be really used as the default
database but it does not matter if you mention the right database in
the track configuration. Still, the observation should be useful in
some way. I'll get back to this problem after few days.

Thanks a lot.

Chandan


On Sat, Jul 2, 2011 at 5:15 PM, Naoki Amano <[hidden email]> wrote:

> Hi,
>
> I also have failed to display BigBed ( and BigWig) file.  However when I
> changed the order of database in conf file,
> BigBed files was shown in GBrowse.
>
> -Fail Case
>
> [GENREAL]
> description = human
> database   = annotaions     <-------- Bio::DB::SeqFeature::Store
> database  =  testbed         <---------Bio::DB::BigBed
>
> --Successful case
> [GENREAL]
> description = human
> database  =  testbed         <---------Bio::DB::BigBed
> database   = annotaions     <-------- Bio::DB::SeqFeature::Store
>
> In my case,  when the order of database for bigbed was last,  the result was
> error.
>
> I don't know your case was same as my case, however if your order of BigBed
> database was last,
> it is worth to change the order of it.
>
> Regards,
>
> Naoki Amano
>
>
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/BigBed-in-gbrowse-tp4516492p4544542.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
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