Annotations from high confidence IsoSeq data

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Annotations from high confidence IsoSeq data

DECKER, KEITH F [AG/1005]

I have a set of high confidence full length transcripts generated via the pacbio IsoSeq pipeline. 

 

Is there a recommended way to pass these transcripts to MAKER and ensure that the corresponding gene models are included in the final annotation?  I also have assembled illumina transcripts, but I’m trying to figure out how to give the IsoSeq transcripts a higher ‘weight’.

 



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Re: Annotations from high confidence IsoSeq data

Carson Holt-2
MAKER doesn’t assign weights to evidence types, but you can look into EVAL which can take MAKER results and produce new models. If you gave your evidence as est= then EVAL can consume that as well since it will be in the GFF3. MAKER3-beta have some integrated support for eval that you can look at using the maker_eval.ctl file to provide weights to EVAL.

—Carson


On Jul 10, 2019, at 12:12 PM, DECKER, KEITH F [AG/1005] <[hidden email]> wrote:

I have a set of high confidence full length transcripts generated via the pacbio IsoSeq pipeline. 
 
Is there a recommended way to pass these transcripts to MAKER and ensure that the corresponding gene models are included in the final annotation?  I also have assembled illumina transcripts, but I’m trying to figure out how to give the IsoSeq transcripts a higher ‘weight’.
 


The information contained in this e-mail is for the exclusive use of the intended recipient(s) and may be confidential, proprietary, and/or legally privileged.  Inadvertent disclosure of this message does not constitute a waiver of any privilege.  If you receive this message in error, please do not directly or indirectly use, print, copy, forward, or disclose any part of this message.  Please also delete this e-mail and all copies and notify the sender.  Thank you.


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