[maker-devel] mising UTRs even with transcript evidence

[Carson Holt]

MAKER needs a little more info about an alignment that may not exist in the GFF3. MAKER2 will reject GFF3 input for UTR generation, but MAKER3 will use it as long as it can generate some of the missing info internally using certain assumptions about the alignment. Also alignments will be rejected for UTR generation that have non-canonical splicing.

—Carson


> On Sep 26, 2021, at 1:54 PM, Childs, Kevin <kchilds at msu.edu> wrote:
> 
> Carson,
> 
> I am helping a student to annotate a genome.  Despite having provided transcript evidence, there are many cases where the MAKER gene models are missing obvious UTRs that are found in the transcripts.  The link below is for a screenshot with some examples.
> 
> https://figshare.com/s/0b29e0b0ac10f868dbe9
> 
> In the figure, there are genes at ~148 kbp, ~152 kbp, ~160 kbp, ~170 kbp that are missing UTRs that should have been predicted by the transcripts in the second track.  The annotation is pretty much riddled with this type of behavior.
> 
> One mea culpa, the transcript data was provided as a gff file, and that file had all transcripts defined with a source of “bed2gff” instead of “est2genome”.  I feel that I had found that to be important during some past annotation work, but it doesn’t explain why many but not all genes have UTRs when evidence is present.
> 
> Thanks.
> 
> Kevin
> 
> ---
> Kevin Childs, PhD
> 
> Assistant Professor - Fixed Term
> Director MSU Genomics Core Facility
> Plant Biology Department
> Michigan State University
> 
> kchilds at msu.edu
> 517-775-2844 (m)
> 517-884-6926 (o)
> 
> http://childslab.plantbiology.msu.edu
> https://rtsf.natsci.msu.edu/genomics/
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20210927/61b743a9/attachment-0003.p7s>