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

[Gloria Rendon]

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
fasta_merge            maker2wap               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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20160226/056aecd1/attachment-0002.html>