Hi Hiram,
Thank you for responding. But when I tried to run it
through the table browzer, i get the following error.
Error File 'ref1.psl.txt' - Error line 6 of custom track: 1
not a recognized sequence (note: sequence names are case
sensitive)
I have also attached the file with just one line on it.
Could you please help?
Thanks,
Preeti
> --- On Sat, 14/11/09, Hiram Clawson <[email protected]>
> wrote:
>
> > From: Hiram Clawson <[email protected]>
> > Subject: Re: [Genome] psltobed.c
> > To: "Sankaranarayanan Preethi" <[email protected]>
> > Cc: [email protected]
> > Date: Saturday, 14 November, 2009, 12:04 PM
> > Good Evening Preethi:
> >
> > This is a program in the kent source tree.
> > http://genome.ucsc.edu/admin/cvs.html
> > http://genome.ucsc.edu/admin/jk-install.html
> >
> > It would be easier to enter your psl file as a custom
> > track into the genome browser, then use the table
> > browser to dump it back to you as a bed file.
> > http://genome.ucsc.edu/goldenPath/help/customTrack.html
> > http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
> >
> > --Hiram
> >
> >
> > Sankaranarayanan Preethi wrote:
> > > Hi,
> > >
> > > I have no idea where should I download this file
> and
> > run. My problem is I have a .psl file. I need to
> convert it
> > to a .bed file. that is all. Could you please help me
> how to
> > do this? I tried checking on the genome browser
> webpage.
> > there is no download... I am confused. please help!
> > >
> > > Thanks,
> > > Preeti
> > >
> > >
> > > Add whatever you love
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> > >
> >
>
>
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match mis- rep. N's Q gap Q gap T gap T gap strand Q
Q Q Q T T T T block
blockSizes qStarts tStarts
match match count bases count bases name
size start end name size start end count
---------------------------------------------------------------------------------------------------------------------------------------------------------------
27 0 0 0 0 0 0 0 +
simulated_der5_p2|1|:1:61124719-61124746 27 0 27 1
247249719 61125138 61125165 1 27, 0,
61125138,
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