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View Process Hh 05

Annotation with Maker

maker -CTL

#——-Genome (Required for De-Novo Annotation)
genome=Ensamble20K/GENOMABROCA.fasta #genome sequence file in fasta format
organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic #——-Re-annotation Using MAKER Derived GFF3
genome_gff= #re-annotate genome based on this gff3 file
est_pass=0 #use ests in genome_gff: 1 = yes, 0 = no
altest_pass=0 #use alternate organism ests in genome_gff: 1 = yes, 0 = no
protein_pass=0 #use proteins in genome_gff: 1 = yes, 0 = no
rm_pass=0 #use repeats in genome_gff: 1 = yes, 0 = no
model_pass=0 #use gene models in genome_gff: 1 = yes, 0 = no
pred_pass=0 #use ab-initio predictions in genome_gff: 1 = yes, 0 = no
other_pass=0 #passthrough everything else in genome_gff: 1 = yes, 0 = no #——-EST Evidence (for best results provide a file for at least one)
est=../Transcriptoma/TRANSCRIPTOMABROCA.fasta #non-redundant set of assembled ESTs in fasta format (classic EST analysis)
est_reads= #unassembled nextgen mRNASeq in fasta format (not fully implemented)
altest= #EST/cDNA sequence file in fasta format from an alternate organism
est_gff= #EST evidence from an external gff3 file
altest_gff= #Alternate organism EST evidence from a separate gff3 file #——-Protein Homology Evidence (for best results provide a file for at least one)
protein= #protein sequence file in fasta format
protein_gff= #protein homology evidence from an external gff3 file #——-Repeat Masking (leave values blank to skip repeat masking)
model_org=all #select a model organism for RepBase masking in RepeatMasker
rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker
repeat_protein=/opt/maker/data/te_proteins.fasta #provide a fasta file of transposable element proteins for RepeatRunner
rm_gff= #repeat elements from an external GFF3 file
prok_rm=0 #forces MAKER to run repeat masking on prokaryotes (don’t change this), 1 = yes, 0 = no #——-Gene Prediction
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species=tribolium #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=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #gene prediction from protein homology (prokaryotes only), 1 = yes, 0 = no
unmask=0 #Also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no #——-Other Annotation Feature Types (features MAKER doesn’t recognize)
other_gff= #features to pass-through to final output from an extenal GFF3 file #——-External Application Behavior Options
alt_peptide=C #amino acid used to replace non standard amino acids in BLAST databases
cpus=4 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI) #——-MAKER Behavior Options
max_dna_len=500000 #length for dividing up contigs into chunks (increases/decreases memory usage)
min_contig=1 #skip genome contigs below this length (under 10kb are often useless)
pred_flank=200 #flank for extending evidence clusters sent to gene predictors
AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)
min_protein=0 #require at least this many amino acids in predicted proteins
alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no
always_complete=0 #force start and stop codon into every gene, 1 = yes, 0 = no
map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no
keep_preds=0 #Add unsupported gene prediction to final annotation set, 1 = yes, 0 = no

maker maker_exe.ctl maker_opts.ctl maker_bopts.ctl

mkdir gff
find GENOMABROCA.maker.output/ -name *.gff -exec cp {} gff \;