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

Sun Feb 3 15:43:42 MST 2019

Hi Morgan,

We had a similar issue with AUGUSTUS underpredicting when using a
BUSCO-derived gene model
https://groups.google.com/d/msg/maker-devel/ocnDG4nq1A8/NyCPzzRgAgAJ

Also, check the number of proteins by each individual predictor. If the
numbers from one of them are off, you may find a possible source of issues.
We didn't have a very good experience with GM, as it used to overpredict an
absurd number of proteins.

Xabi

On Mon, 4 Feb 2019 at 06:15, 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
>
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>

-- 
Xabier Vázquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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