Thanks for letting me know. I'm also forwarding this galaxy-dev, so the thread
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!
> On Thu, May 12, 2011 at 10:54 AM, Anton Nekrutenko <an...@bx.psu.edu> wrote:
> "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.
> galaxy team
> Anton Nekrutenko
> 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
> > ___________________________________________________________
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