[ensembl-dev] multiple stops in Taestivum annotation [MIPS v2.1, Ensembl v22]
Arnaud Kerhornou
arnaud at ebi.ac.uk
Thu May 1 12:20:06 BST 2014
Hi Ksenia,
Further to Will's reply, I had a look at the gff3 we provide, and the
warnings you get.
It seems that they only occur for the first exon of the transcripts, in
the case of transcripts with more than one exon.
In the gff3 we generate, the exon phase for these first exons is not set.
According to the GFF3 specs, this is valid,
http://www.sequenceontology.org/gff3.shtml
The phase gets represented for the CDS features.
The only case I would envisage this information useful, is when there is
no 5'UTR, and the start of the gene is missing, then the first exon can
have a phase flag.
Anyway, we'll look into rationalising the way we represent phase info
for exon features for the next release to avoid any confusion.
Let us know if the Ensembl Variant Effect Predictor (VEP) works for you.
Best regards,
Arnaud
On 01/05/2014 11:01, Will McLaren wrote:
> Hello Ksenia,
>
> Have you considered using the VEP? This is Ensembl's equivalent to
> snpEff, and offers many features that snpEff does not. It also does
> not depend on using these GFF files.
>
> http://www.ensembl.org/info/docs/tools/vep/script/index.html
>
> To set up for use with wheat, simply run the installer as follows:
>
> perl INSTALL.pl -u
> ftp://ftp.ensemblgenomes.org/pub/plants/release-22/vep/ -s
> triticum_aestivum -a ac
>
> Regarding your issue with the GFF3 file, we think this may be due to a
> problem with exon phase in the file, though someone from the Ensembl
> Genomes project may be able to comment further.
>
> HTH
>
> Will McLaren
> Ensembl Variation
>
>
> On 30 April 2014 23:08, Ksenia Krasileva <krasileva at ucdavis.edu
> <mailto:krasileva at ucdavis.edu>> wrote:
>
> Dear Ensembl team,
>
> I am currently working with a GFF3 annotation of Triticum aestivum
> (MIPS v2.1, Ensembl v22).
> ftp://ftp.ensemblgenomes.org/pub/plants/release-22/gff3/triticum_aestivum/Triticum_aestivum.IWGSP1.22.gff3.gz
>
> In our study, we are examining single nucleotide polymorphism
> variants in wheat and their effect on protein coding regions using
> SNPeff 3.5d (build 2014-03-05)
>
> I see a warning message from SNPeff
> "WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS" in 17,834 genes. Below
> are 10 examples of genes that have this warning and 10 that do not.
>
> Do you know what might be causing such warning? Or refer me to
> someone who can help?
>
> Thank you in advance.
>
> Best wishes,
>
> Ksenia
>
> --
> Ksenia Krasileva, PhD
>
> Post Doctoral Scholar
> USDA NIFA Fellowship
> The Dubcovsky Lab
>
> Department of Plant Sciences
> University of California, Davis
> 124 Robbins Hall
> Davis, CA 95616
> krasileva at ucdavis.edu <mailto:krasileva at ucdavis.edu>
>
> SNPeff data:
>
> 10 examples without warnings:
> IWGSC_CSS_5BS_scaff_1487662 672 Kronos381 G A
> 40.0 Pass
> seed_avail=Kronos381;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G280||Traes_5BS_38DA1CBC61.E1|||transcript:Traes_5BS_38DA1CBC61.2|1|1)
> IWGSC_CSS_5BS_scaff_1537048 1688 Kronos244 C T
> 40.0 Pass
> seed_avail=Kronos244;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A58V||CDS:Traes_5BS_B2CD001D1.2|||transcript:Traes_5BS_B2CD001D1.2|2|1)
> IWGSC_CSS_5BS_scaff_1537048 1718 Kronos439 C T
> 40.0 Pass
> seed_avail=Kronos439;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A68V||CDS:Traes_5BS_B2CD001D1.2|||transcript:Traes_5BS_B2CD001D1.2|2|1)
> IWGSC_CSS_5BS_scaff_1646558 3136 Kronos684 G A
> 40.0 Pass
> seed_avail=Kronos684;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T115||Traes_5BS_E2116F66A.E1|||transcript:Traes_5BS_E2116F66A.1|1|1)
> IWGSC_CSS_5BS_scaff_168385 2625 Kronos2646 G A
> 40.0 Pass
> seed_avail=Kronos2646;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E18K||Traes_5BS_91BD3E004.E1|||transcript:Traes_5BS_91BD3E004.1|1|1)
> IWGSC_CSS_5BS_scaff_168385 2666 Kronos390 C T
> 40.0 Pass
> seed_avail=Kronos390;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A31||Traes_5BS_91BD3E004.E1|||transcript:Traes_5BS_91BD3E004.1|1|1)
> IWGSC_CSS_5BS_scaff_168385 2714 Kronos166 G A
> 40.0 Pass
> seed_avail=Kronos166;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E47||Traes_5BS_91BD3E004.E1|||transcript:Traes_5BS_91BD3E004.1|1|1)
> IWGSC_CSS_5BS_scaff_1712494 1012 Kronos447 C T
> 40.0 Pass
> seed_avail=Kronos447;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G681R||Traes_5BS_6004CA039.E3|||transcript:Traes_5BS_6004CA039.1|1|1)
> IWGSC_CSS_5BS_scaff_1712494 2037 Kronos2214 G A
> 40.0 Pass
> seed_avail=Kronos2214;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S339F||Traes_5BS_6004CA039.E3|||transcript:Traes_5BS_6004CA039.1|1|1)
> IWGSC_CSS_5BS_scaff_1712494 2086 Kronos199 G A
> 40.0 Pass
> seed_avail=Kronos199;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P323S||Traes_5BS_6004CA039.E3|||transcript:Traes_5BS_6004CA039.1|1|1)
>
>
> 10 Examples with warnings:
> IWGSC_CSS_1BS_scaff_1134305 892 Kronos2092 G A
> 40.0 Pass
> seed_avail=Kronos2092;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V123I||Traes_1BS_9AD3B3BE2.E22|||transcript:Traes_1BS_9AD3B3BE2.1|4|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),SPLICE_SITE_REGION(LOW|||||Traes_1BS_9AD3B3BE2.E22|||transcript:Traes_1BS_9AD3B3BE2.1|4|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
> IWGSC_CSS_1BS_scaff_1134305 5997 Kronos2711 C T
> 40.0 Pass
> seed_avail=Kronos2711;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A806V||Traes_1BS_9AD3B3BE2.E22|||transcript:Traes_1BS_9AD3B3BE2.1|18|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
> IWGSC_CSS_1BS_scaff_1260855 1972 Kronos375 G A
> 40.0 Pass
> seed_avail=Kronos375;EFF=SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R266||Traes_1BS_91DEF138E.E1|||transcript:Traes_1BS_91DEF138E.1|6|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
> IWGSC_CSS_1BS_scaff_1280056 767 Kronos166 C T
> 40.0 Pass
> seed_avail=Kronos166;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N93||Traes_1BS_984B78A41.E3|||transcript:Traes_1BS_984B78A41.1|3|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
> IWGSC_CSS_1BS_scaff_1420918 702 Kronos209 G A
> 40.0 Pass
> seed_avail=Kronos209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G138E||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
> IWGSC_CSS_1BS_scaff_1420918 871 Kronos166 G A
> 40.0 Pass
> seed_avail=Kronos166;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R194||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
> IWGSC_CSS_1BS_scaff_1420918 912 Kronos209 G A
> 40.0 Pass
> seed_avail=Kronos209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G208E||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
> IWGSC_CSS_1BS_scaff_1420918 5050 Kronos2553 G A
> 40.0 Pass
> seed_avail=Kronos2553;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V692I||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|11|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),UPSTREAM(MODIFIER||1659|||Traes_1BS_587F929ED.E1|||transcript:Traes_1BS_587F929ED.1||1)
> IWGSC_CSS_1BS_scaff_1912213 607 Kronos910 G A
> 40.0 Pass
> seed_avail=Kronos910;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S59N||Traes_1BS_0039045F7.E21|||transcript:Traes_1BS_0039045F7.2|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
> IWGSC_CSS_1BS_scaff_1975885 313 Kronos684 G A
> 40.0 Pass
> seed_avail=Kronos684;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G25R||Traes_1BS_CC1B13C13.E32|||transcript:Traes_1BS_CC1B13C13.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
>
> --
> Ksenia Krasileva, PhD
>
> Post Doctoral Scholar
> USDA NIFA Fellowship
> The Dubcovsky Lab
>
> Department of Plant Sciences
> University of California, Davis
> 124 Robbins Hall
> Davis, CA 95616
> krasileva at ucdavis.edu <mailto:krasileva at ucdavis.edu>
>
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