[maker-devel] Why would MAKER generate a large gff3?

[Carson Holt]

> On May 1, 2015, at 2:53 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> There is probably something weird about the way you are running it.  For example did you give it the raw RNA-seq reads instead of the assembled reads?
> 
> The total size of the final GFF3 will be all genes + all evidence alignments + the assembly fasta (concatenated at the end per GFF3 format specifications).  You can remove the fasta or the evidence alignments from the file using the options found in gff3_merge.  
> 
> —Carson
> 
>> 
>> From: John Cornelius <jcornel3 at asu.edu <mailto:jcornel3 at asu.edu>>
>> Subject: Why would MAKER generate a large gff3?
>> Date: May 1, 2015 at 2:46:45 PM MDT
>> To: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>> 
>> 
>> Hello, I'm using MAKER to generate a new annotation for an organism without an officially published genome (but it does exist and I'm using it). The current annotation is primarily predictive and I'm adding RNA-Seq evidence to improve it. However, after the initial run and the following two runs with SNAP, the gff3 file generated is 24 GB in size while the old annotation file is only 82 Mb. Should is be that large? Also, what is the best way to analyze a new annotation to figure out if it is actually in decent shape? Thanks. 
>> 
>> -- 
>> John Cornelius
>> MCB PhD Candidate
>> Arizona State University
>> 
>> 
>> 
>> From: maker-devel-request at yandell-lab.org <mailto:maker-devel-request at yandell-lab.org>
>> Subject: confirm d8a6466a8a63fe2312cc2ce7f79739414020644e
>> Date: May 1, 2015 at 2:47:11 PM MDT
>> 
>> 
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