[maker-devel] Re-annotation, fewer gene predictions

[Carson Holt]

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.

—Carson



> On Feb 3, 2019, at 12:13 PM, morgan sobol <morgan_starr_s at live.com> wrote:
> 
> Hello, 
> 
> 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. 
> 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. 
> 
> 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. 
> 
> 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?
> 
> Thanks,
> Morgan S. 
> 
> maker_opts.log
> #-----Genome (these are always required)
> genome=/work/Geomicrobiology/msobol/IODP_329_SPG/1368D2H1/repeatmasker/unicycler/1368D_unicycler_contigs.fasta.masked #genome sequence (fasta file or$
> organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic
> 
> #-----Re-annotation Using MAKER Derived GFF3
> maker_gff=/work/Geomicrobiology/msobol/IODP_329_SPG/1368D2H1/maker/1368D_2H1_contigs.fasta.maker.output/1368D_2H1_contigs.fasta.all.gff #MAKER derive$
> est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no
> altest_pass=1 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
> protein_pass=1 #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= #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=/work/Geomicrobiology/msobol/IODP_329_SPG/uniprot_sprot.fasta  #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= #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=0 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
> 
> #-----Gene Prediction
> snaphmm= #SNAP HMM file
> gmhmm=/home/msobol/genemark/68D_2/output/gmhmm.mod #GeneMark HMM file
> augustus_species=1368D_uni #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=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 = 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=1 #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=1 #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=1 #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=1 #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=0 #remove all data from previous run before retrying, 1 = yes, 0 = no
> clean_up=0 #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
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20190213/9051057c/attachment-0003.html>