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
