[maker-devel] Est2Genome Problems

[Jason Gallant]

Hi Folks,


I’ve nearly succeeded at getting MAKER to run on AWS— I’ve been checking the output files, and have noticed that none of my RNAseq data was incorporated on the run.  I used Cufflinks to perform alignments of libraries from several tissues, ran the accessory script cufflinks2gff3 for each tissue, then concatenated the resulting gff3 files.  I even ran the accessory script gff3merge to check that the resulting file was properly formatted.


For options, I set est2genome=1 and est_gff=cufflinks.gff.  I only get protein2genome and repeatmasker evidence in my resulting maker gff3 file, and the genes predicted by these.  Is there another option that I need to enable in order to use my est_gff file?  I’m trying to get a set of genes to train the predictors for my next step.


Any help would (as always) be greatly appreciated!


Best,
Jason Gallant

—
Dr. Jason R. GallantAssistant Professor
Room 38 Natural Sciences
Department of Zoology
Michigan State University
East Lansing, MI 48824
jgallant at msu.edu

office: 517-884-7756
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150203/82bd337e/attachment-0002.html>