[maker-devel] some problems using MAKER

[赵越]

Hi all,

Recently I'm using MAKER to annotate a single chromosome of rice as a
pre-experiment. And I'm confronting some problems. After the annotation
when I run the evaluation of eval between my result and gold standard, the
gene sensitivity&specificity is only around 20%. And after I added the gff3
file maker made itself to run maker again, I found that the result is worse
than 20%.

My input is a Trinity-processed RNA-seq file and a protein file.  I chose
snap, augustus and genemark as ab initio predictors.

I paste my maker_opts.ctl here:

#-----Genome (these are always required)
genome=chr12.fasta #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=chr12.gff #MAKER derived GFF3 file
est_pass=1 #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=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=rna-seq_trinity.fasta #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=Osativa_193_peptide.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=Rice #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=rice #SNAP HMM file
gmhmm=/lustre/home/clswcc/yzhao/MAKER/maker/exe/genemark_hmm_euk_linux_64/ehmm/o_sativa.mod
#GeneMark HMM file
augustus_species=arabidopsis #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff=augus.gff3 #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
trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no


snoscan_rrna= #rRNA file to have Snoscan find snoRNAs
unmask=1 #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)


Could you help me? Thank you !!!



-- 

*Yue Zhao (Jerry)*

Bachelor Candidate of Plant Biotechnology

Researcher in UCLA-CSST program

Shanghai Jiao Tong University, Shanghai

*jerryzhaosjtu at gmail.com <jerryzhaosjtu at gmail.com>*
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