<div dir="ltr">Hi all,<div><br></div><div>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%. </div><div><br></div><div>My input is a Trinity-processed RNA-seq file and a protein file. I chose snap, augustus and genemark as ab initio predictors.</div><div><br></div><div>I paste my maker_opts.ctl here:</div><div><br></div><div><div>#-----Genome (these are always required)</div><div>genome=chr12.fasta #genome sequence (fasta file or fasta embeded in GFF3 file)</div><div>organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic</div><div><br></div><div>#-----Re-annotation Using MAKER Derived GFF3</div><div>maker_gff=chr12.gff #MAKER derived GFF3 file</div><div>est_pass=1 #use ESTs in maker_gff: 1 = yes, 0 = no</div><div>altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no</div><div>protein_pass=1 #use protein alignments in maker_gff: 1 = yes, 0 = no</div><div>rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no</div><div>model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no</div><div>pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no</div><div>other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no</div><div><br></div><div>#-----EST Evidence (for best results provide a file for at least one)</div><div>est=rna-seq_trinity.fasta #set of ESTs or assembled mRNA-seq in fasta format</div><div>altest= #EST/cDNA sequence file in fasta format from an alternate organism</div><div>est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file</div><div>altest_gff= #aligned ESTs from a closly relate species in GFF3 format</div><div><br></div><div>#-----Protein Homology Evidence (for best results provide a file for at least one)</div><div>protein=Osativa_193_peptide.fa #protein sequence file in fasta format (i.e. from mutiple oransisms)</div><div>protein_gff= #aligned protein homology evidence from an external GFF3 file</div><div><br></div><div>#-----Repeat Masking (leave values blank to skip repeat masking)</div><div>model_org=Rice #select a model organism for RepBase masking in RepeatMasker</div><div>rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker</div><div>repeat_protein= #provide a fasta file of transposable element proteins for RepeatRunner</div><div>rm_gff= #pre-identified repeat elements from an external GFF3 file</div><div>prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no</div><div>softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)</div><div><br></div><div>#-----Gene Prediction</div><div>snaphmm=rice #SNAP HMM file</div><div>gmhmm=/lustre/home/clswcc/yzhao/MAKER/maker/exe/genemark_hmm_euk_linux_64/ehmm/o_sativa.mod #GeneMark HMM file</div><div>augustus_species=arabidopsis #Augustus gene prediction species model</div></div><div><div>fgenesh_par_file= #FGENESH parameter file</div><div>pred_gff=augus.gff3 #ab-initio predictions from an external GFF3 file</div><div>model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)</div><div>est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no</div><div>protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no</div><div>trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no </div><div>snoscan_rrna= #rRNA file to have Snoscan find snoRNAs</div><div>unmask=1 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no</div><div><br></div><div>#-----Other Annotation Feature Types (features MAKER doesn't recognize)</div><div>other_gff= #extra features to pass-through to final MAKER generated GFF3 file</div><div><br></div><div>#-----External Application Behavior Options</div><div>alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases</div><div>cpus=16 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)</div></div><div><br></div><div><br></div><div>Could you help me? Thank you !!!<br><div><br></div><div><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><p style="margin:0cm 0cm 0.0001pt;text-align:justify;font-family:Calibri,sans-serif"><b><i><span lang="EN-US" style="font-size:10pt;color:rgb(38,38,38)">Yue Zhao (Jerry)</span></i></b><br></p><p style="margin:0cm 0cm 0.0001pt;text-align:justify;font-family:Calibri,sans-serif"><span lang="EN-US" style="font-size:10pt;color:black">Bachelor Candidate of Plant Biotechnology<u></u><u></u></span></p><p style="margin:0cm 0cm 0.0001pt;text-align:justify;font-family:Calibri,sans-serif"><span lang="EN-US" style="font-size:10pt;color:black">Researcher in UCLA-CSST program<u></u><u></u></span></p><p style="margin:0cm 0cm 0.0001pt;text-align:justify;font-family:Calibri,sans-serif"><span lang="EN-US" style="font-size:10pt;color:black">Shanghai Jiao Tong University, Shanghai<u></u><u></u></span></p><p style="margin:0cm 0cm 0.0001pt;text-align:justify;font-family:Calibri,sans-serif"><u><span lang="EN-US" style="color:black"><a href="mailto:jerryzhaosjtu@gmail.com" style="color:rgb(17,85,204)" target="_blank">jerryzhaosjtu@gmail.com</a></span></u></p></div></div></div></div>
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