<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">One thing you can also do is use old models as protein= input and run the protein2genome option just to see where things align. You may find that not all old models are recoverable in the new assembly. Fewer genes in the new assembly may mean redundant/duplicate contigs were collapse and split contigs were joined resulting in multiple gene fragments becoming a unified single model. Make sure to always review contigs in a browser to see how models and evidence correlate.</div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""></div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">—Carson</div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""></div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 3, 2019, at 12:13 PM, morgan sobol <<a href="mailto:morgan_starr_s@live.com" class="">morgan_starr_s@live.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Hello,
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<div class="">I previously used Maker to annotate two different fungal genomes that were created using Illumina sequences only. For these genomes, I had over 11,000 genes predicted. </div>
<div class="">I recently obtained PacBio sequences for the same genomes, so I created two hybrid assemblies. Both assemblies were very familiar in length and completed number of orthologs to the Illumina only assembly, but had much fewer, but longer contigs. </div>
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<div class="">I re-ran Maker using the settings below. For one of my genomes, I got around 11,000 genes predicted again, as expected. However, for the other genome, I am continuously getting ~4,400 predicted genes. </div>
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<div class="">I am asking for help as to how I can determine why I keep getting fewer predicted genes for only one of my genomes, even though I ran them the same?</div>
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<div class="">Thanks,</div>
<div class="">Morgan S. </div>
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<div class="">maker_opts.log</div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Genome (these are always required)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">genome=/work/Geomicrobiology/msobol/IODP_329_SPG/1368D2H1/repeatmasker/unicycler/1368D_unicycler_contigs.fasta.masked #genome sequence (fasta file or$</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Re-annotation Using MAKER Derived GFF3</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">maker_gff=/work/Geomicrobiology/msobol/IODP_329_SPG/1368D2H1/maker/1368D_2H1_contigs.fasta.maker.output/1368D_2H1_contigs.fasta.all.gff #MAKER derive$</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">altest_pass=1 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">protein_pass=1 #use protein alignments in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----EST Evidence (for best results provide a file for at least one)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">est= #set of ESTs or assembled mRNA-seq in fasta format</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">altest= #EST/cDNA sequence file in fasta format from an alternate organism</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">altest_gff= #aligned ESTs from a closly relate species in GFF3 format</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Protein Homology Evidence (for best results provide a file for at least one)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">protein=/work/Geomicrobiology/msobol/IODP_329_SPG/uniprot_sprot.fasta #protein sequence file in fasta format (i.e. from mutiple oransisms)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">protein_gff= #aligned protein homology evidence from an external GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Repeat Masking (leave values blank to skip repeat masking)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">model_org= #select a model organism for RepBase masking in RepeatMasker</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">repeat_protein= #provide a fasta file of transposable element proteins for RepeatRunner</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">rm_gff= #pre-identified repeat elements from an external GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">softmask=0 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Gene Prediction</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">snaphmm= #SNAP HMM file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">gmhmm=/home/msobol/genemark/68D_2/output/gmhmm.mod #GeneMark HMM file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">augustus_species=1368D_uni #Augustus gene prediction species model</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">fgenesh_par_file= #FGENESH parameter file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">pred_gff= #ab-initio predictions from an external GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">protein2genome=1 #infer predictions from protein homology, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">snoscan_rrna= #rRNA file to have Snoscan find snoRNAs</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Other Annotation Feature Types (features MAKER doesn't recognize)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">other_gff= #extra features to pass-through to final MAKER generated GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----External Application Behavior Options</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----MAKER Behavior Options</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">min_contig=1 #skip genome contigs below this length (under 10kb are often useless)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">pred_flank=200 #flank for extending evidence clusters sent to gene predictors</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">pred_stats=1 #report AED and QI statistics for all predictions as well as models</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">min_protein=0 #require at least this many amino acids in predicted proteins</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">keep_preds=1 #Concordance threshold to add unsupported gene prediction (bound by 0 and 1)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">split_hit=10000 #length for the splitting of hits (expected max intron size for evidence alignments)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">single_exon=1 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">tries=2 #number of times to try a contig if there is a failure for some reason</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">clean_up=0 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">TMP= #specify a directory other than the system default temporary directory for temporary files</span></div>
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