Maker protocols Pmajor

This page describes the various rounds of Maker-based annotations for the Parus major (Great Tit) genome.

Round 1

Rationale

For this round no P. major-based ESTs were available. Zebrafinch (T. guttata) is the closest relative for which a reasonably complete gene-model set is available. As a first pass, it was decided to let gene predictions be driven by ab-inititio predictions rather than by Zebrafinch EST.

Maker settings

content of maker_opts.ctl:

#-----Genome (these are always required)
 genome=Pam.fa #genome sequence (fasta file or fasta embeded in GFF3 file)
 organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic
 
 #-----Re-annotation Using MAKER Derived GFF3
 maker_gff= #MAKER derived GFF3 file
 est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no
 altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
 protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no
 rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no
 model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no
 pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no
 other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no
 
 #-----EST Evidence (for best results provide a file for at least one)
 est= #set of ESTs or assembled mRNA-seq in fasta format
 altest= Taeniopygia_guttata.taeGut3.2.4.74.cdna.all.fa #EST/cDNA sequence file in fasta format from an alternate organism
 est_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= Taeniopygia_guttata.taeGut3.2.4.74.pep.all.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)
 model_org=Metazoa #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= #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= /cm/shared/apps/WUR/ABGC/snap/snap-2013-11-29/HMM/mam54.hmm #SNAP HMM file
 gmhmm= #GeneMark HMM file
 augustus_species= chicken #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 #infer predictions from protein homology, 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= #extra features to pass-through to final MAKER generated GFF3 file
 
 #-----External Application Behavior Options
 alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases
 cpus=16 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
 
 #-----MAKER Behavior Options
 max_dna_len=100000 #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
 pred_stats=0 #report AED and QI statistics for all predictions as well as models
 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 #extra steps to force start and stop codons, 1 = yes, 0 = no
 map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no
 keep_preds=0 #Concordance threshold to add unsupported gene prediction (bound by 0 and 1)
 
 split_hit=10000 #length for the splitting of hits (expected max intron size for evidence alignments)
 single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no
 single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'
 correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes
 
 tries=2 #number of times to try a contig if there is a failure for some reason
 clean_try=1 #remove all data from previous run before retrying, 1 = yes, 0 = no
 clean_up=1 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no
 TMP= #specify a directory other than the system default temporary directory for temporary files

See also

Maker pipeline as installed on the B4F cluster