Hello Breman,
The latest version of GBrowse takes several formats
(http://modencode.oicr.on.ca/gbrowse2/annotation_help.html):
* BED
* GFF
* GFF3
* Wiggle (WIG) (for dense quantitative data)
* BAM or SAM (for sequence alignment data)
If you are using a GBrowse installation that supports SAM/BAM, then it's
definitely recent enough to support BED format, too. If needed, the utility
pslToBed is in the kent source tree or pre-compiled here:
http://hgdownload.cse.ucsc.edu/admin/exe/
Making the psl to sam converter more robust is on our do-to list, as it would
be a better option once complete. For now, the BED option is the recommendation
based on your feedback.
Thank you for your patience while we worked out a solution,
Jennifer
------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group
----- "Bremen Braun" <[email protected]> wrote:
> From: "Bremen Braun" <[email protected]>
> To: "Jennifer Jackson" <[email protected]>
> Cc: [email protected]
> Sent: Friday, January 15, 2010 10:28:40 AM GMT -08:00 US/Canada Pacific
> Subject: Re: [Genome] Alignment tools question
>
> Hi Jennifer,
> Thank you for the list. However, I notice many of these tools are
> tailored
> to next-gen short read sequencing. The sequences I'm dealing with are
> BAC
> end sequences. Has anyone used the psl to sam converter with
> confidence?
>
> On Fri, Jan 15, 2010 at 12:15 PM, Jennifer Jackson <[email protected]>
> wrote:
>
> > Hello Breman,
> >
> > A list of alignment tools that directly output SAM output is
> available
> > here:
> > http://samtools.sourceforge.net/swlist.shtml
> >
> > We hope this resource is helpful to you,
> > Jennifer jackson
> >
> >
> > ------------------------------------------------
> > Jennifer Jackson
> > UCSC Genome Bioinformatics Group
> >
> > ----- "Bremen Braun" <[email protected]> wrote:
> >
> > > From: "Bremen Braun" <[email protected]>
> > > To: [email protected]
> > > Sent: Friday, January 15, 2010 9:16:42 AM GMT -08:00 US/Canada
> Pacific
> > > Subject: [Genome] Alignment tools question
> > >
> > > Hello,
> > > I am wondering if Blat is recommended for my situation. I am
> hoping
> > > to
> > > display backend sequences mapped against genomic sequences and to
> view
> > > the
> > > differences using SAM. What comparison tool would you recommend? I
> see
> > > as of
> > > yet samtools doesn't convert psl to sam but there is a low
> priority
> > > open
> > > task to do so. The task difficulty has been described as easy, so
> > > surely
> > > there's someone that has already performed this task?
> > >
> > > Thanks,
> > > Bremen Braun
> > > _______________________________________________
> > > Genome maillist - [email protected]
> > > https://lists.soe.ucsc.edu/mailman/listinfo/genome
> >
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
