Re: [AMOS-help] negative gaps in AMOScmp

[Brian H. <bh...@br...>]

Hi Adam,

What I'm trying to do is to come up with a single scaffold that best 
corresponds to the reference sequence.  For the case with the negative 
gaps, I'm just trimming off that number of bases (and quals) from the 
corresponding contig, and reconstructing the scaffold sequence (and 
corresponding qual file) myself.   This seems better than the 
alternative, which is having two slightly overlapping contigs that map 
to the reference.  Again, obtaining a single scaffold sequence that's 
the best representation of the scaffold-mappings is my goal.

Thanks,

-b



Adam Phillippy wrote:
> Hi Brian,
> I'm not sure if bank2scaff handles this correctly, but it probably 
> does (please check). If the -G/-N options work as expected and you set 
> -G 1 and -N 10, then any gap of 0 or less should receive 10 N's (-N) 
> in between the two contigs.
>
> Negative scaffold gaps usually indicate something fishy is going on, 
> so I would hesitate to assemble the two contigs together without more 
> information. In amoscmp the scaffolding is based entirely on the 
> alignment to the reference. So if there is a reasonably sized 
> insertion in the target genome, I could imagine how two contigs would 
> be constructed on either side of the inserted sequence and the mapping 
> to the reference indicates a slight overlap. BUT, just because they 
> overlap doesn't mean they should be assembled together as some 
> additional sequence may belong in between that wasn't assembled 
> because it didn't match the reference.
>
> Best,
> -Adam
>
>
>
> On Mon, Jun 1, 2009 at 8:13 PM, Brian Haas <bh...@br... 
> <mailto:bh...@br...>> wrote:
>
>     Hi Adam, Mike,
>
>     I found that there are cases where AMOScmp is reporting a negative gap
>     length in the scaffolding information.
>
>     For example:
>     AMOScmp scaffolding information:
>      >153054_Staphylococcus_USA300_subsp 2 1520 1517
>     1_153054_Staphylococcus_USA300_subsp BE 738 -8
>     2_153054_Staphylococcus_USA300_subsp BE 782 0
>
>
>     In these cases, the scaffold generated by
>     $(BINDIR)/bank2scaff -f -g -G 0 $(BANK) > $(SCAFFOLD)
>
>     appears to be just joining the contigs together.  When the gap size is
>     zero, that's fine, but for the negative gaps, should it be either:
>     -assembling the two contigs together in the first place
>     or
>     -removing the overlap when building the scaffold
>     ?
>
>     Thanks!
>
>     -b
>
>     --
>     Brian J. Haas
>     Manager, Bioinformatics Outreach, Genome Annotation and Analysis
>     The Broad Institute
>     http://broad.mit.edu/~bhaas <http://broad.mit.edu/%7Ebhaas>
>
>
>
>
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-- 
Brian J. Haas
Manager, Bioinformatics Outreach, Genome Annotation and Analysis
The Broad Institute
http://broad.mit.edu/~bhaas