[maker-devel] mapping cDNA to updated genome

[Carson Holt]

Also if you have multiple alignments of the same cDNA, you can use the score column of the mRNA feature to see which aligns best. If they have the same score, you will have to disambiguate manually or just remove all copies.

—Carson


> On Aug 31, 2016, at 10:10 AM, Michael Campbell <michael.s.campbell1 at gmail.com> wrote:
> 
> Hi Prashant,
> 
> I’m almost positive that the additional genes are coming from multiply aligning cDNAs. Did you repeat mask your genome before mapping things forward?
> 
> Another thought, what kind of whole genome duplications has your plant been through. it may be that the multiple alignments are to pseudogenes is some stage of decay. If that is the case it would probably be safe to keep the the gene from longest/best aligned cDNA.
> 
> Thanks,
> Mike
>> On Aug 31, 2016, at 10:35 AM, Prashant S Hosmani <psh65 at cornell.edu <mailto:psh65 at cornell.edu>> wrote:
>> 
>> Hi All,
>> 
>> I am working on updating a plant genome annotation. I would like to map genes from previous annotation to a new genome build. There is a protocol about this in Campbell et al 2014, current protocols in bioinformatics (basic protocol 4 - Mapping annotations to a new assembly). I followed that protocol exactly with setting est_forward=1. But in output I’m getting large number of genes. My input cDNA fasta contains ~35K genes and after mapping there are ~58K genes. 
>> 
>> I’m using maker version 3.0. There are few changes in the genome and I’m not expecting many changes in the mapping previous genes.
>> 
>> Please let me know if there are any other parameters to control mapping of EST’s. I was hoping to get similar number of genes mapped on to new assembly with very few changes.
>> 
>> Thank you for your help in advance.
>> Prashant
>> 
>> 
>> Prashant Hosmani
>> Sol Genomics Network
>> Boyce Thompson Institute, Ithaca, NY, USA
>> 
>> 
>> 
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