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MAKER

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User support and development list for the MAKER genome annotation pipeline. MAKER is a part of the Generic Model Organism Database (GMOD) project.

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Topics (1189)
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maker-level google group by Linnie Linnie
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by Linnie Linnie
Help debugging a MAKER result by Lior Glick
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by Lior Glick
NCBI now accepts GFF by Daniel Ence-2
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by Daniel Ence-2
Plant and Animal Genome Conference 2019 by Carson Hinton Holt
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by Carson Hinton Holt
Re-annotation of a previous annotation with "est2genome=1" by dupim
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by Carson Holt-2
Maker annotation small DNA fragments by Philippine De Boisse...
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by Carson Holt-2
MAKER chooser algorithm by Timo Metz
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by Carson Holt-2
Maker ignores evidence and just returns gffs with genome contigs by Ganote, Carrie L
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by Carson Holt-2
maker_map_ids issue by Vining, Kelly
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by Carson Holt-2
Running MAKER using MPI over SGE scheduler with multiple nodes by Lior Glick
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by Carson Holt-2
Maker 3 versus older versions by Steven Sullivan
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by Carson Holt-2
How sensitive is MAKER to redundant/partial transcripts? by Lior Glick-2
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by Carson Holt-2
Annotation of a new variant within a species by Lior Glick
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by Carson Holt-2
Few alternative isoforms when alt_splice=0 by roscito
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by Carson Holt-2
Maker Error : Thread 1 terminated abnormally.. André Machado <andremmachado25@gmail.com> AttachmentsJun 26 (8 days ago) to maker-devel Hi , First of all thanks for your efforts in Maker pipeline. Its a tremendous help for the people that works with genomes. In the last 4 days i have broke my head.. with an error .. but still without a solution. I found this old thread: https://groups.google.com/forum/#!msg/maker-devel/X2-76BH9gvg/rU4kLJ3B6tsJ Seems to be a quite similar... but don't point to a specific solution. I have run maker with the data test and all runned ok. Maker finalize the entire process without errors. Recently, i’m trying to aplly my own data on MPI cluster. But this error, frequently occurred. Thread 1 terminated abnormally: ../dna.maker.output/mpi_blastdb/dna%2Efa.mpi.1/dna%2Efa.mpi.1.0 --> rank=8, hostname=compute-0-1.local, at ../Analysis/Geno/maker/bin/maker line 1451 thread 1. --> rank=8, hostname=compute-0-1.local deleted:0 hits deleted:0 hits preparing ab-ini by André Machado
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by Carson Holt-2
Maker Error : Thread 1 terminated abnormally.. by André Machado
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by Carson Holt-2
map_forward=1 not mapping reference ID's to output correctly by kapeel
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by Carson Holt-2
How sensitive is MAKER to redundant/partial transcripts? by Lior Glick
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by Carson Holt-2
Genemark XXX.mod files by Jennifer Anderson
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by Jason Stajich-4
Best annotation set failure (auto_annotator.pm line 1774) by Greer Dolby
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by Greer Dolby
Filtering gene models based on eAED scores by Federico López
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by Carson Holt-2
Transcript & protein fasta sequence id/name collisions by Stein, Joshua
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by Stein, Joshua
Merge warning = 1 by Jennifer Anderson
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by Carson Holt-2
largest genome annotated? by Andor J Kiss
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by Carson Holt-2
how to input a masked assembly for annotation into Maker by Valerie Soza
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by Carson Holt-2
Building MAKER with specific perl version by Ksenia Lavrichenko
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by Carson Holt-2
large UTR overhang by Timo Metz
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by Carson Holt-2
databases supported with ipr_update_gff script by Valerie Soza
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by Carson Holt-2
MAKER beta not inferring gene models from protein evidence by Timo Metz
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by Timo Metz
MAKER v3 ERROR: Failed while processing all repeats by kapeel
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by kapeel
keep_preds=0 but some gene models have anyway an AED equal to 1. by Jacques Dainat-4
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by Carson Holt-2
MAKER v3 ERROR: Failed while processing all repeats by kapeel
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by kapeel
Error in maker perl module by Jiapeng Chen
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by Carson Holt-2
how to output masked genome from MAKER by Valerie Soza
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by Carson Holt-2
substr outside of string in PhatHits_utils.pm by Ole Kristian Tørrese...
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by Jacques Dainat-4
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