[maker-devel] MAKER/3.00.0-beta: missing some accessory scripts

[Carson Holt]

You should be using maker2eval_gtf. The scripts you mention were actually deprecated in MAKER 2.10 onwards (about 5 years ago). You may be looking at old documentation.

—Carson


> On Feb 26, 2016, at 3:14 PM, Gloria Rendon <gloriarendon at gmail.com> wrote:
> 
> Hello,
> 
> My name is Gloria Rendon. I work at the Carle Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign.
> 
> In recent months we used MAKER/3.00.0-beta to generate annotations (in GFF3 format) for a de-novo assembly that we produced in-house for the Taro plant.
> 
> As part of the same project, I need to run now an analysis with RNA seq data for the same Tarospecies. 
> I am going to use STAR for the alignment step and I need to provide the annotations file in GTF format, not in GFF3 format as I currently have.
> 
> In order to perform the GFF3->GTF conversion I was planning to run some of the accessory scripts that come with MAKER
> 
> add_utr_start_stop_gff 
> gff3_2_gtf
> 
> However I just noticed that my installation of MAKER is missing those two scripts. 
> This is how the MAKER/bin folder looks like now:
> 
> $ ls /home/groups/hpcbio/apps/maker/maker-3.00.0-beta/bin/
> AED_cdf_generator.pl   ipr_update_gff          maker_map_ids
> cegma2zff              iprscan2gff3            map2assembly
> chado2gff3             maker                   map_data_ids
> compare_gff3_to_chado  maker2chado             map_fasta_ids
> cufflinks2gff3         maker2eval_gtf          map_gff_ids
> evaluator              maker2jbrowse           match2gene.pl <http://match2gene.pl/>
> fasta_merge            maker2wap               quality_filter.pl <http://quality_filter.pl/>
> fasta_tool             maker2zff               tophat2gff3
> genemark_gtf2gff3      maker_functional_fasta
> gff3_merge             maker_functional_gff
> 
> 
> btw, earlier versions of MAKER that are also installed on our cluster as also missing those scripts.
> 
> Could you please tell me how to remedy the situation?
> Do you have executables  of the two scripts that you can share with me?
> OR 
> Do I need to re-install MAKER with special configuration options?
> 
> Thank you very much for the attention to this matter.
> 
> Sincerely,
> 
> Gloria
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