<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I’d have to see the two GFF3 files you are using for your comparison.<div class=""><br class=""></div><div class="">However one thing that comes to mind is that you may be unfamiliar with eval’s output. Eval provides several levels of strictness in the report at the gene, transcript, exon, and base pair levels. If you are using the gene level strictness in the report for example, then a single base pair difference in any of the transcripts will cause the entire gene to be considered a miss-match. You really only should use the base pair level SN/SP strictness for your comparison which will be in the eval report. In the most extreme case an exon level SN/SP strictness may be used, but in general no gold standard dataset is considered perfect enough to use the gene level SN/SP (or usually even the exon level strictness).<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Dec 31, 2014, at 6:48 PM, 赵越 <<a href="mailto:jerryzhaosjtu@gmail.com" class="">jerryzhaosjtu@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi all,<div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">I paste my maker_opts.ctl here:</div><div class=""><br class=""></div><div class=""><div class="">#-----Genome (these are always required)</div><div class="">genome=chr12.fasta #genome sequence (fasta file or fasta embeded in GFF3 file)</div><div class="">organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic</div><div class=""><br class=""></div><div class="">#-----Re-annotation Using MAKER Derived GFF3</div><div class="">maker_gff=chr12.gff #MAKER derived GFF3 file</div><div class="">est_pass=1 #use ESTs in maker_gff: 1 = yes, 0 = no</div><div class="">altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no</div><div class="">protein_pass=1 #use protein alignments in maker_gff: 1 = yes, 0 = no</div><div class="">rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no</div><div class="">model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no</div><div class="">pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no</div><div class="">other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no</div><div class=""><br class=""></div><div class="">#-----EST Evidence (for best results provide a file for at least one)</div><div class="">est=rna-seq_trinity.fasta #set of ESTs or assembled mRNA-seq in fasta format</div><div class="">altest= #EST/cDNA sequence file in fasta format from an alternate organism</div><div class="">est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file</div><div class="">altest_gff= #aligned ESTs from a closly relate species in GFF3 format</div><div class=""><br class=""></div><div class="">#-----Protein Homology Evidence (for best results provide a file for at least one)</div><div class="">protein=Osativa_193_peptide.fa #protein sequence file in fasta format (i.e. from mutiple oransisms)</div><div class="">protein_gff= #aligned protein homology evidence from an external GFF3 file</div><div class=""><br class=""></div><div class="">#-----Repeat Masking (leave values blank to skip repeat masking)</div><div class="">model_org=Rice #select a model organism for RepBase masking in RepeatMasker</div><div class="">rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker</div><div class="">repeat_protein= #provide a fasta file of transposable element proteins for RepeatRunner</div><div class="">rm_gff= #pre-identified repeat elements from an external GFF3 file</div><div class="">prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no</div><div class="">softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)</div><div class=""><br class=""></div><div class="">#-----Gene Prediction</div><div class="">snaphmm=rice #SNAP HMM file</div><div class="">gmhmm=/lustre/home/clswcc/yzhao/MAKER/maker/exe/genemark_hmm_euk_linux_64/ehmm/o_sativa.mod #GeneMark HMM file</div><div class="">augustus_species=arabidopsis #Augustus gene prediction species model</div></div><div class=""><div class="">fgenesh_par_file= #FGENESH parameter file</div><div class="">pred_gff=augus.gff3 #ab-initio predictions from an external GFF3 file</div><div class="">model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)</div><div class="">est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no</div><div class="">protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no</div><div class="">trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no </div><div class="">snoscan_rrna= #rRNA file to have Snoscan find snoRNAs</div><div class="">unmask=1 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no</div><div class=""><br class=""></div><div class="">#-----Other Annotation Feature Types (features MAKER doesn't recognize)</div><div class="">other_gff= #extra features to pass-through to final MAKER generated GFF3 file</div><div class=""><br class=""></div><div class="">#-----External Application Behavior Options</div><div class="">alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases</div><div class="">cpus=16 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Could you help me? Thank you !!!<br class=""><div class=""><br class=""></div><div class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-family: Calibri, sans-serif;" class=""><b class=""><i class=""><span lang="EN-US" style="font-size:10pt;color:rgb(38,38,38)" class="">Yue Zhao (Jerry)</span></i></b><br class=""></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 10pt;" class="">Bachelor Candidate of Plant Biotechnology<u class=""></u><u class=""></u></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 10pt;" class="">Researcher in UCLA-CSST program<u class=""></u><u class=""></u></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 10pt;" class="">Shanghai Jiao Tong University, Shanghai<u class=""></u><u class=""></u></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-family: Calibri, sans-serif;" class=""><u class=""><span lang="EN-US" style="" class=""><a href="mailto:jerryzhaosjtu@gmail.com" style="color:rgb(17,85,204)" target="_blank" class="">jerryzhaosjtu@gmail.com</a></span></u></div></div></div></div></div>
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