[Bioperl-l] Mapping Blast results

[shalabh sharma]

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
>