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<div class="moz-cite-prefix">Hi Ksenia,<br>
<br>
Further to Will's reply, I had a look at the gff3 we provide, and
the warnings you get.<br>
It seems that they only occur for the first exon of the
transcripts, in the case of transcripts with more than one exon.<br>
In the gff3 we generate, the exon phase for these first exons is
not set.<br>
<br>
According to the GFF3 specs, this is valid,<br>
<a class="moz-txt-link-freetext" href="http://www.sequenceontology.org/gff3.shtml">http://www.sequenceontology.org/gff3.shtml</a><br>
The phase gets represented for the CDS features.<br>
<br>
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.<br>
Anyway, we'll look into rationalising the way we represent phase
info for exon features for the next release to avoid any
confusion.<br>
<br>
Let us know if the Ensembl Variant Effect Predictor (VEP) works
for you.<br>
<br>
Best regards,<br>
Arnaud<br>
<br>
On 01/05/2014 11:01, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX2e+UqGghqW3tdbTuhoNbG9TjJ5zHtGPeEwiURk=JuycQ@mail.gmail.com"
type="cite">
<div dir="ltr">Hello Ksenia,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/tools/vep/script/index.html"
target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/index.html</a><br>
</div>
<div><br>
</div>
<div>To set up for use with wheat, simply run the installer as
follows:</div>
<div><br>
</div>
<div>perl INSTALL.pl -u <a moz-do-not-send="true"
href="ftp://ftp.ensemblgenomes.org/pub/plants/release-22/vep/"
target="_blank">ftp://ftp.ensemblgenomes.org/pub/plants/release-22/vep/</a>
-s triticum_aestivum -a ac<br>
</div>
<div><br>
</div>
<div>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.</div>
<div>
<br>
</div>
<div>HTH</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 30 April 2014 23:08, Ksenia
Krasileva <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:krasileva@ucdavis.edu" target="_blank">krasileva@ucdavis.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div style="font-family:arial,sans-serif;font-size:13px">Dear
Ensembl team,</div>
<div style="font-family:arial,sans-serif;font-size:13px">
<br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">I
am currently working with a GFF3 annotation of Triticum
aestivum (MIPS v2.1, Ensembl v22).</div>
<div style="font-family:arial,sans-serif;font-size:13px"> <span
dir="ltr"><a moz-do-not-send="true"
href="ftp://ftp.ensemblgenomes.org/pub/plants/release-22/gff3/triticum_aestivum/Triticum_aestivum.IWGSP1.22.gff3.gz"
target="_blank">ftp://ftp.ensemblgenomes.org/pub/plants/release-22/gff3/triticum_aestivum/Triticum_aestivum.IWGSP1.22.gff3.gz</a></span><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<span style="font-family:arial,sans-serif;font-size:13px">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)</span><span
style="font-family:arial,sans-serif;font-size:13px">
<div>
<br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Do you know what might be causing such warning? Or
refer me to someone who can help?</div>
<div><br>
</div>
<div>Thank you in advance.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Ksenia</div>
<div><br>
</div>
</span><span
style="font-family:arial,sans-serif;font-size:13px">
<div><span style="font-family:arial;font-size:small">-- </span><br
style="font-family:arial;font-size:small">
<div dir="ltr"
style="font-family:arial;font-size:small">Ksenia
Krasileva, PhD<br>
<br>
Post Doctoral Scholar<br>
USDA NIFA Fellowship<br>
The Dubcovsky Lab<br>
<br>
Department of Plant Sciences<br>
University of California, Davis<br>
124 Robbins Hall<br>
Davis, CA 95616<br>
<a moz-do-not-send="true"
href="mailto:krasileva@ucdavis.edu"
target="_blank">krasileva@ucdavis.edu</a></div>
</div>
<div dir="ltr" style="font-family:arial;font-size:small"><br>
</div>
<div style="font-family:arial;font-size:small">
SNPeff data:</div>
<div style="font-family:arial;font-size:small"><br>
</div>
10 examples without warnings:</span><br
style="font-family:arial,sans-serif;font-size:13px">
<div style="font-family:arial,sans-serif;font-size:13px">
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)</div>
<div style="font-family:arial,sans-serif;font-size:13px">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)</div>
<div style="font-family:arial,sans-serif;font-size:13px">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)</div>
<div style="font-family:arial,sans-serif;font-size:13px">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)</div>
<div style="font-family:arial,sans-serif;font-size:13px">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)</div>
<div style="font-family:arial,sans-serif;font-size:13px">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)</div>
<div style="font-family:arial,sans-serif;font-size:13px">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)</div>
<div style="font-family:arial,sans-serif;font-size:13px">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)</div>
<div style="font-family:arial,sans-serif;font-size:13px">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)</div>
<div style="font-family:arial,sans-serif;font-size:13px">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)</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">10
Examples with warnings:<br>
<div>
<div>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)</div>
<div>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)</div>
<div>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)</div>
<div>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)</div>
<div>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)</div>
<div>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)</div>
<div>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)</div>
<div>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)</div>
<div>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)</div>
<div>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)</div>
<span class="HOEnZb"><font color="#888888">
</font></span></div>
</div>
<span class="HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div dir="ltr">Ksenia Krasileva, PhD<br>
<br>
Post Doctoral Scholar<br>
USDA NIFA Fellowship<br>
The Dubcovsky Lab<br>
<br>
Department of Plant Sciences<br>
University of California, Davis<br>
124 Robbins Hall<br>
Davis, CA 95616<br>
<a moz-do-not-send="true"
href="mailto:krasileva@ucdavis.edu"
target="_blank">krasileva@ucdavis.edu</a><br>
</div>
</font></span></div>
<br>
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<br>
</blockquote>
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