[maker-devel] Maker2 gff file output

[Mark Yandell]

Hi Blake,

I'be forwarded this onto the maker_devel list, they can help you  more there.

regarding your comment g 'When I view the output of many contigs in Apollo, there is many times where 3 or 4 models show close to identical gene structure, but the final maker output does not contain that gene call.  ' Those calls are in the output files, but there are in a  different multifasta file; there are  non-overalpping ab intio models.  Another way is to set the config flag to allow MAKEr to use unspliced EST and RNA-seq alignments as evidence,

I'be forwarded this onto the maker_devel list, they can help you  more there.

cheers,

--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: Blake Hovde [hovdebt at uw.edu]
Sent: Tuesday, March 19, 2013 2:35 PM
To: Mark Yandell
Subject: Maker2 gff file output

Hi Dr. Yandell,

I am currently running MAKER2 on a new algal genome and am running
into a couple of problems that I would like your input on the genome
size is ~60Mb and is currently in ~3100 contigs.
First, I am having trouble doing multiple iterations of hmm training
with SNAP due to the fact that I have so many gff output files in the
datastore (1 for each contig in my draft genome). not just a single
gff output that seems to be in the examples and tutorials I have
followed thus far. Is there a way to combine all of my gff files
together to make use of the SNAP hmm training or re-annotation?

Second, Using multiple lines of evidence (augustus, genemarkES, RNAseq
data, and COGs based on homology searches) I am having a hard time
getting a lot of maker gene calls.  It seems that the calling is too
stringent in many cases.  When I view the output of many contigs in
Apollo, there is many times where 3 or 4 models show close to
identical gene structure, but the final maker output does not contain
that gene call.  Do you have any suggestions on how to lower the
stringency of the MAKER output so that more genes will be called?  In
some cases I am getting less than 3000 gene calls in the final output.
 Where an Augustus model trained on Chlamydamonas will return ~15000.

Thanks very much for your help!

Sincerely,
Blake Hovde
Graduate Student
Department of Genome Sciences
University of Washington