[maker-devel] Incorporating cufflinks in maker

[Holmer, Rens]

Hi,

Great follow-ups! I indeed also use Genome-Guided Trinity to generate transcripts in parallel to cufflinks. I find that trinity denovo is actually often more noisy than cufflinks/tophat/transdecoder. For instance trinity often transcripts in intron regions because of spurious pre-mRNA reads.
Currently I use BRAKER in stead of augustus, and the results are great. One thing to note is that augustus within maker does not provide the same results as the BRAKER output. I suspect this is because maker sends additional hints to the gene predictors on the fly. In my case BRAKER seems more accurate the the maker-augustus.

So I provide BRAKER output as pred-gff, transdecoder output as model-gff and trinity transcripts as EST.

Would love to hear comments!

Cheers,

Rens

On 03 Apr 2015, at 07:37, Jason Stajich <jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>> wrote:

I also echo this - also has anyone given BRAKER a try as an alternative gene prediction input from augustus with hints through MAKER?
http://bioinf.uni-greifswald.de/augustus/downloads/


Jason Stajich
jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>

On Thu, Apr 2, 2015 at 10:36 AM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:
I actually find it better to process data with Trinity.  Cufflinks results tend to be too noisy, and any sensitivity lost by using an assembly approach instead of an alignment based approach is generally rescued by protein data.

—Carson


> On Mar 30, 2015, at 12:12 AM, Holmer, Rens <rens.holmer at wur.nl<mailto:rens.holmer at wur.nl>> wrote:
>
> Hi maker team,
>
> I am currently working on a project where we want to incorporate quite a lot of RNA-seq into our annotation. Currently I see two options:
>
> Provide the cufflinks output as EST-gff
> Process cufflinks output with TransDecoder (find ORFs, annotate UTR, etc) and provide this as either pred_gff or model_gff
>
> What would you suggest, and what would be the required formatting for both options?
>
> Thanks in advance,
>
> Rens Holmer
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