Rich, You can convert base quality scores using the FASTQ Groomer tool. Note that Galaxy tools typically work with Sanger (Phred+33) quality scores.
Good luck, J. On Aug 29, 2011, at 10:48 PM, Richard Mark White wrote: > Hi, > Thanks very much. I've tried this, but one thing I have noticed is that if > I do the initial mapping with BWA vs. Bowtie the # of variants I get is much > larger with BWA. I have seen mention on the web that you need to change the > quality score annotation for BWA before running SAMtools, but not sure > precisely how to do this. any thoughts? > > Rich > > > From: Jeremy Goecks <jeremy.goe...@emory.edu> > To: Richard Mark White <whit...@yahoo.com> > Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu> > Sent: Sunday, August 28, 2011 2:18 PM > Subject: Re: [galaxy-user] rna-seq mutation detection > > Rich, > > Given that you're analyzing your RNA-seq data using Galaxy, I'd guess that > you're using Tophat to map your reads onto on reference genome. If this is > the case, then you can use the BAM files produced by Tophat to generate > variation data for each sample. The variation tools that you'll want to look > at are > > [NGS: SAM Tools-->]Generate Pileup > [NGS: GATK Tools-->]Unified Genotyper (only avaiable on our test server and > still in beta) > > The outputs for each tool produce a consensus base for each potential > variation site, and you can compare the consensus base for each sample to > look for differences. > > If you're doing de novo assembly of your RNA-seq data to look for variation, > you'll need to use tools that are not currently available in Galaxy. > > Good luck, > J. > > > On Aug 18, 2011, at 12:22 PM, Richard Mark White wrote: > >> Hi, >> I am trying to look at differences between two RNA-seq samples to see if >> there are mutations in one of them relative to the other (i.e. not in >> comparison to a reference genome). Does anyone know of a way to do this >> within galaxy? Any help is appreciated! >> >> rich >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ > > >
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
