[Bioperl-l] Mapping Blast results

[Scott Cain]

Ah, not readable as in "my eyes can't make anything out" not as in
"the file is corrupted and my image viewing software won't open it."
That's two different things.  Yes, I imagine making the panel taller
would help, but in Bio::Graphics::Panel you don't have direct control
of the panel height.  Instead, you can try changing the value of the
bump parameter.  Try +1 or +2 to see if that helps.  See the perldoc
for Bio::Graphics::Panel for more info.

For converting blast results to GFF, see the bioperl script bp_search2gff.pl.

Scott


On Tue, Feb 2, 2010 at 2:05 PM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hi,
>     Its not readable as the reads are so closed that i can just see one
> vertical line. Do i need to increase the panel size?
> I am not sure that how to convert blast results to gff file.
> Thanks
> Shalabh
> On Tue, Feb 2, 2010 at 1:55 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Shalabh,
>>
>> Please keep your responses on the list.
>>
>> A few things:
>>
>> * While it interesting that the resulting png isn't readable (and I
>> don't know why--perhaps the script is silently crashing?), I have to
>> wonder if a graphic with 1500 hits for a particular gene will be of
>> that much use anyway?  Perhaps, but it seems to me that 500 will do
>> just as well as 1500 :-)
>>
>> * When you say you don't know how to map hits to a particular gene,
>> what is the hang up?  Coordinate mapping?  Converting blast results to
>> GFF?
>>
>> Scott
>>
>>
>> On Tue, Feb 2, 2010 at 1:47 PM, shalabh sharma
>> <shalabh.sharma7 at gmail.com> wrote:
>> > Hi,
>> >      thanks for your quick reply.
>> > Actually i am getting a png file but its not readable (there are about
>> > 1500
>> > hits).
>> > I have a working Gbrowse on my system but i don't know how i can map my
>> > blast reads to a particular gene.
>> > Thanks
>> > Shalabh
>> >
>> > On Tue, Feb 2, 2010 at 1:34 PM, Scott Cain <scott at scottcain.net> wrote:
>> >>
>> >> Hi Shalabh,
>> >>
>> >> When you say it's not working, what do you mean?  Presumably, you
>> >> could write a script that uses Bio::DB::SeqFeature::Store if speed is
>> >> the problem, but if you wanted to go that far, your time would
>> >> probably be better spent installing GBrowse.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Tue, Feb 2, 2010 at 10:16 AM, shalabh sharma
>> >> <shalabh.sharma7 at gmail.com> wrote:
>> >> > Hi,
>> >> >    I am trying to map blast results on a gene. I am using
>> >> > Bio::Graphics
>> >> >    http://bioperl.org/wiki/HOWTO:Graphics
>> >> >
>> >> > This is working fine for small blast files but not for large blast
>> >> > file
>> >> > with
>> >> > lot of hits. Is there any way i can use this for large blast files?
>> >> >
>> >> > Thanks
>> >> > Shalabh
>> >> > _______________________________________________
>> >> > Bioperl-l mailing list
>> >> > Bioperl-l at lists.open-bio.org
>> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research