Thanks for letting me know. I'm also forwarding this galaxy-dev, so the thread in complete.
Thanks, anton Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On May 12, 2011, at 2:30 PM, Katie Hyma wrote: > Hi Anton, > > You're right, sorry for the false alarm. After a more careful inspection of > my data I'm pleased to say that I was wrong and that everything with galaxy > is fine, it turns out that the company that generated the previous data had > generated the error; good think I checked those results, I had just assumed I > that my analysis had the error! > > Katie > > On Thu, May 12, 2011 at 10:54 AM, Anton Nekrutenko <an...@bx.psu.edu> wrote: > Katie: > "Filter pileup" outputs 0-based coordinates if you use the " Convert > coordinates to intervals" option. So the issue may be related to aaChanges > tools. Can you give us a specific example, so we can track things down. > > Thanks! > > anton > galaxy team > > > > Anton Nekrutenko > http://nekrut.bx.psu.edu > http://usegalaxy.org > > > > On May 12, 2011, at 10:37 AM, Katie Hyma wrote: > > > Hi all, > > > > I ran into this problem, and thought others might run in to it as well: > > When using bowtie and samtools, positions are formatted with a 1-base > > offset, whereas interval format requires 0-base offset. > > Recently, I used the 'Filter pileup on coverage and SNPs' tool with the > > 'convert coordinates to intervals' option, and used the output with the > > 'aaChanges' tool to detect amino acid changes. > > In the aaChanges output there was an off-by-one discrepancy with a previous > > analysis, which brought this problem to my attention. > > Should the 'Filter pileup' tool be changed to produce output with 0-base > > offset when interval format is selected, since interval format is defined > > as having 0-base output? It seems that others might run into the same > > problem, and it would be an easy one to miss. > > Although the pileup format is now deprecated, the same problem might occur > > if/when the change to VCF format occurs, as it also uses 1-base offset. It > > also may be a problem for other tools that use interval format as an input, > > expecting a 0-based position. > > > > Best, > > Katie > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > > > http://lists.bx.psu.edu/ > >
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