[maker-devel] maker predicting only part of a gene

[Debojyoti Das]

Hi,

I am working on a non-model reptile species.   I tried running maker with
est2genome=1 and protein2genome=1 with the following evidence:

1. est=transcriptome.fasta (de novo assembled)
2. protein in fasta format from two related species.


 I keep getting predictions where gene models identify multi-exon genes but
fail to incorporate all the exons even though they are present on the
scaffolds. The fact that in the predicted gene models some exons were
correctly identified while missing others even though the entire gene is
present on the scaffolds, we checked this by loading the annotation in IGV
Viewer.

Since we are not completely confident of our transciptome assembly, we
thought of using cDNA from a closely related species.
1. altest="cDNA in fasta format from a related species"
2. protein in fasta format from two related species.

However, when I do this I get the error
*"ERROR: You must provide some form of EST evidence to use est2genome as a
predictor."*

Interestingly, if I switch est2genome off (setting it to zero) maker starts
running.

Any suggestions on how to proceed.

Best,
Debojyoti
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