[maker-devel] maker_coor behaviour

[Mikael Brandström Durling]

Hi,

in a previous thread, the maker_coor feature for ETSs was mentioned. I have been trying it out, without using it for mapping gene names. I have placed these ESTs by other means, an thought the maker_coor feature would be a good use of this a priori knowledge. My major problem i try to solve is that I find that some ESTs where I know where they should be aligned, are not recruited to that position by maker’s blastn->exonerate method (I find them on other scaffolds). So I thought maker_coor with the est_forward behavior (as described) would be a good option to force my evidence onto the correct position, instead of ending up supporting or braking other models. However, as soon as I run with maker_coor tagged est sequences, no est2genome evidence appears in the final gff3 file. The blastn evidence is there when est_forward is disabled, but as expected, there is no blastn evidence when est_forward is turned on. It seems though as the evidence is used, as the QI lines indicate EST support for both splice sites as well as exon alignments, but I have no way to visualize and/or evaluate the congruence of evidence and models. Would it be possible to tweak Maker into outputting the est2genome alignments when est_forward/maker_coor is used? I couldn’t figure myself where in the code this was handled.

I could of course do my own exonerate alignments of these ESTs and feed them into maker as est_gff, but if maker already has the machinery to to this, I thought it would be a good idea to use it.

Thanks,
Mikael