Apologies if you receive this email twice: I originally posted it with an attachment, then tried (unsuccessfully) to cancel the posting as the message was too big.
Hi I'm trying to load gff (version 3) into Artemis for the first time (I've previously had good success loading data from GenBank files), and I'm having trouble displaying mRNA and CDS features. I'm using a test gff file containing 1 gene. The feature entries in the gff are: ##gff-version 3 contig_1574 . contig 1 105753 . . . ID=contig_1574;Name=contig_1574; contig_1574 maker mRNA 73760 75490 . + . ID=m1;Name=m1; contig_1574 maker exon 73760 73887 3.73 + . ID=m1:exon:1919;Parent=m1; contig_1574 maker exon 73968 75490 33.33 + . ID=m1:exon:1920;Parent=m1; contig_1574 maker CDS 73825 73887 0 + 0 ID=m1:cds:1864;Parent=m1; contig_1574 maker CDS 73968 74417 0 + 0 ID=m1:cds:1865;Parent=m1; The mRNA feature isn't displayed in the Overview/DNA views at all, and the feature key "mRNA" is greyed out in the Feature List. The individual CDS/exon features are displayed, but they aren't linked in the Overview and DNA views (whereas when I loaded from GenBank in the past, I see CDSs within a single gene linked by a line). I assumed the "Parent" qualifier in exon/CDS entries would result in linking multipart features. The only message in the log is " 30 Mar 09:35 - BAM & VCF not visible." I'm running v13 via WebStart. If anyone would like the entire gff (including the contig fasta sequence) then please email me. Any ideas on what I'm doing wrong? Thanks (: Anar ____________________________ Anar Khan Bioinformatician T +64 3 489 9154 E anar.k...@agresearch.co.nz AgResearch Limited Invermay Agricultural Centre Puddle Alley, Private Bag 50034, Mosgiel, New Zealand T +64 3 489 3809 F +64 3 489 3739 www.agresearch.co.nz Farming Food and Health. First Te Ahuwhenua Te Kai me te Whai Ora. Tuatahi ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================
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