Full description of commands used for annotate de Mahi mahi genome, with SNAP and AUGUSTUS Install MAKER: https://github.com/Yandell-Lab/maker
We used the following tutoraials as base for the annotation. 1.https://darencard.net/blog/2017-05-16-maker-genome-annotation/ 2.http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018
Prior launching Maker the following programs are run independently
- blastp with a database of closely related species
- interpro scan with https://www.uniprot.org/help/downloads Swiss-Prot
- RepeatMasker https://www.repeatmasker.org/cgi-bin/WEBRepeatMasker
- AUGUSTUS https://github.com/Gaius-Augustus/Augustus
- SNAP https://hpc.nih.gov/apps/snap.html
The scripts for AUGUSTUS and SNAP are for run separatedly The script MAKER_round1 is a round using RNAseq data, similar species proteins with out gene prediction support The script MAKER_round2 is a round using gene prediction (Augustus or SNAP) Remember to evaluate each round, is important to at least run MAKER 3 times
Run the following commands after each round to evaluate: Count number of genes $cat your.gff | awk '{ if ($3 == "gene") print $0 }' | awk '{ sum += ($5 - $4) } END { print NR, sum / NR }' On MAKER/bin $perl AED_cdf_generator.pl -b 0.025 your.gff
Finally run the merge_final_make.sh to obtain finall outputfiles