[ensembl-dev] multiple stops in Taestivum annotation [MIPS v2.1, Ensembl v22]
Will McLaren
wm2 at ebi.ac.uk
Thu May 1 11:01:14 BST 2014
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> 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
>
> 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
>
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