Genome information:
- ~50M nt
- 2300+ contigs
- No pre-trained parameters in Augustus
- There are several well annotated RefSeq genomes of this genus.
- There are several RNA-seq data of this genus, but not in this species.
My current strategy:
EST evidence:
- I selected many RNA-seq data that include as many species as
possible, and de novo assembled these data using
Trinity
. - Only the longest transcripts were saved.
- All transcript files were catenated into a
Total_transcript.fasta
file, andcd-hit-est
was used to reduce data size with options-c 0.8 -n 5 -s 0.8
.
Protein evidence
All fungal proteins from SwissProt was download and reduced using
cd-hit
with options-c 0.8 -n 5 -s 0.8
.Proteinsets from RefSeq genomes of this genus were download, catenated, reduced using same methods.
I planed to annotate genome using Maker2
with above Evidence.
I have a doubt about my strategy: Maker2 calls Augustus to ab-initio annotation, but no pre-trained model. How should I do to solve this?
Anyone else could share your valuable suggestions? Thanks anyway.