Configure your maker project : The maker_opts.ctl file in detail:
When executing the command “maker -CTL” MAKER creates 3 control files. Of these, only maker_opts.ctl is of concern to us. Have a look at the following sections and fill in the information as shown:
\#-----Genome (these are always required)
genome=**genome.fa** #genome sequence (fasta file or fasta embeded in GFF3 file)
organism\_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic
...
\#-----EST Evidence (for best results provide a file for at least one)
est= #set of ESTs or assembled mRNA-seq in fasta format
altest= #EST/cDNA sequence file in fasta format from an alternate organism
**est\_gff=est2genome.gff** #aligned ESTs or mRNA-seq from an external GFF3 file
altest\_gff= #aligned ESTs from a closly relate species in GFF3 format
...
\#-----Protein Homology Evidence (for best results provide a file for at least one)
**protein=protein-set1.fa,protein-set2.fa** #protein sequence file in fasta format (i.e. from mutiple oransisms)
protein\_gff= #aligned protein homology evidence from an external GFF3 file
...
\#-----Repeat Masking (leave values blank to skip repeat masking)<br/>
**model\_org=** #select a model organism for RepBase masking in RepeatMasker
rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker
**repeat\_protein=** #provide a fasta file of transposable element proteins for RepeatRunner
rm\_gff=**repeatmasker.gff** #pre-identified repeat elements from an external GFF3 file
prok\_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
...
\#-----Gene Prediction
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus\_species= #Augustus gene prediction species model
fgenesh\_par\_file= #FGENESH parameter file
pred\_gff= #ab-initio predictions from an external GFF3 file
model\_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
**est2genome=1** #infer gene predictions directly from ESTs, 1 = yes, 0 = no
**protein2genome=1** #infer predictions from protein homology, 1 = yes, 0 = no
trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no
snoscan\_rrna= #rRNA file to have Snoscan find snoRNAs
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = noTo better understand the different parameters you can have a look here