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 <anton@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

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