<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="">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.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 26, 2016, at 3:14 PM, Gloria Rendon <<a href="mailto:gloriarendon@gmail.com" class="">gloriarendon@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hello,<br class=""><br class="">My name is Gloria Rendon. I work at the Carle Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign.<br class=""><br class="">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.<br class=""><br class="">As part of the same project, I need to run now an analysis with RNA seq data for the same Tarospecies. <br class="">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.<br class=""><br class="">In order to perform the GFF3->GTF conversion I was planning to run some of the accessory scripts that come with MAKER<br class=""><br class=""><span style="background-color:rgb(255,255,0)" class="">add_utr_start_stop_gff <br class="">gff3_2_gtf</span><br class=""><br class="">However I just noticed that my installation of MAKER is missing those two scripts. <br class="">This is how the MAKER/bin folder looks like now:<br class=""><br class="">$ ls /home/groups/hpcbio/apps/maker/maker-3.00.0-beta/bin/<br class="">AED_cdf_generator.pl ipr_update_gff maker_map_ids<br class="">cegma2zff iprscan2gff3 map2assembly<br class="">chado2gff3 maker map_data_ids<br class="">compare_gff3_to_chado maker2chado map_fasta_ids<br class="">cufflinks2gff3 maker2eval_gtf map_gff_ids<br class="">evaluator maker2jbrowse <a href="http://match2gene.pl/" class="">match2gene.pl</a><br class="">fasta_merge maker2wap <a href="http://quality_filter.pl/" class="">quality_filter.pl</a><br class="">fasta_tool maker2zff tophat2gff3<br class="">genemark_gtf2gff3 maker_functional_fasta<br class="">gff3_merge maker_functional_gff<br class=""><br class=""><br class="">btw, earlier versions of MAKER that are also installed on our cluster as also missing those scripts.<br class=""><br class=""><span style="background-color:rgb(255,255,0)" class="">Could you please tell me how to remedy the situation?<br class="">Do you have executables of the two scripts that you can share with me?<br class=""></span></div><span style="background-color:rgb(255,255,0)" class="">OR </span><br class=""><span style="background-color:rgb(255,255,0)" class="">Do I need to re-install MAKER with special configuration options?</span><div class=""><br class="">Thank you very much for the attention to this matter.<br class=""><br class="">Sincerely,<br class=""><br class="">Gloria<br class=""></div></div>
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