[maker-devel] maker annotation with cufflinks output

[Daniel Ence]

Hi Dhivya, 

I think there a few numbers that could be helpful to understand what's happening here. 

How many transcripts did Trinity assembly the RNA-seq data into? Also, you had 29,000 transcripts from cufflinks, but fewer from MAKER when you gave it the cufflinks data. How many transcripts did MAKER identify with the cufflinks data? Did you still get more than the 10,000 transcripts that you found with just the Trinity data?

A key part of MAKER's approach to genome annotation that might be affecting it's performance is that it only annotates a gene where there is both evidence (like your RNA-seq data) and an ab-initio prediction. If a prediction is unsupported by the evidence, then MAKER won't annotate a gene and if evidence aligns where there's no prediction, MAKER won't annotate a gene either. What ab-initio predictors are you using and have they been trained specific genome?

You can force MAKER to automatically promote evidence alignments to a gene model by setting the est2genome option to 1, but that will usually give you many false positives. 

Try rerunning it with either the Trinity data or the Cufflinks data and with est2genome set to 1, and let us know how that affects the MAKER results. 

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of dhivya arasappan [darasappan at gmail.com]
Sent: Thursday, January 30, 2014 11:18 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] maker annotation with cufflinks output

Hello,

I am trying to annotate a 200 mb plant genome for which I have a very
good assembly.

I tried to denovo assemble RNA-seq data using trinity and ran maker
using my genome assembly and the trinity results.  I did not get as
many transcripts as expected, around 10,000 transcripts.

So, I decided to try a different approach.  I did a genome assisted
assembly of the RNA-seq data using tophat/cufflinks. This pipeline
generated 21,000 genes, 29,000 transcripts.  I then ran maker using my
genome assembly and the cufflinks result.  I get much less number of
transcripts as a result.

If cufflinks found 29000 transcripts by mapping to the genome, I'm
confused as to why maker is not finding the same.

Any suggestions would be appreciated.

Thanks
Dhivya


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