[maker-devel] Inquiry about using Exonerate through Maker

[Xin Huang]

Hi,

I have a question regarding the use of Exonerate for cDNA alignment to
genomic scaffolds through Maker.

We first did a blastn search to find out which genomic scaffolds a cDNA
sequence aligns to. There are two scaffolds we figured that host the gene
of interest. So we picked these two scaffolds as the reference genome
sequence in the maker_opts.ctl file. I used the default settings in
maker_bopts.ctl. In the maker_exe.ctl file, the Ab-initio Gene Prediction
Algorithms section has only snap installed. In the maker_opts.ctl file, I
indicated the path to the EST sequence right after "est=" under EST
Evidence, skipped RepeatMasker (when included, only the repeat masking
information was shown in the GFF files) to only do the blast and exonerate,
set "est2genome=1" and left other options at default. In the directory
where we put the Maker output (the control files are all in this
directory), I ran the Maker pipeline using "<path_to_maker> maker_opts.ctl
maker_bopts.ctl maker_exe.ctl". It turned out that there is no alignment
information in the scaffold GFF3 file, just a plain figure indicating that
the scaffold is a contig. Then I tried to use the entire genome scaffold
set as the reference genome and reran the pipeline, still getting the same
results in terms of the Exonerate alignments. Please see the example of a
GFF3 file generated:

##gff-version 3
scaffold3928    .       contig  1       172176  .       .       .
ID=scaffold3928;Name=scaffold3928
###
##FASTA
>scaffold3928
<scaffold_sequence_omitted>

What do I need to adjust to get the alignment information into the GFF file
so I can upload into a genome browser as tracks?

Thank you very much for considering my inquiry.

Sincerely,

Xin Huang
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