Re: [AMOS-help] AMOScmp and empty output

[Adam P. <aph...@gm...>]

Hi Florent,
Can you post the .conflict file, or a portion of it if the whole thing is
too big? I should be able to tell from that. It's possible it could be a
trimming problem.

Thanks,
-Adam



On Wed, Jul 7, 2010 at 1:05 AM, Florent Angly <flo...@gm...>wrote:

> Hi all,
>
> I have Sanger sequences that I try to map on a reference consensus
> sequence assembled using an external assembler. I am using AMOScmp for
> the mapping I am encountering problems. AMOScmp runs without crashing
> but the desired output files are empty.
>
> The nucmer step of AMOScmp produces >2000 entries in the .delta file. I
> think that the problem is at the next step, casm-layout, that seem to
> generate a .conflict file with as many entries as in the .delta file. It
> also generates a .layout file that is empty.
>
> Any idea what is wrong and how to fix it?
>
> Thanks,
>
> Florent
>
>
>
>
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