<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 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 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 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 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 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 href="mailto:krasileva@ucdavis.edu" target="_blank">krasileva@ucdavis.edu</a><br></div>
</font></span></div>
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<br></blockquote></div><br></div>