<div dir="ltr">Thanks a lot. <div><div><a href="mailto:dev@ensembl.org">dev@ensembl.org</a> is very good mailing list to me </div><div><br></div><div><br></div><div><br></div><div><div style="font-size:12.8000001907349px">Regards</div><span class="" style="font-size:12.8000001907349px"><font color="#888888"><div><br></div><div>namchul</div></font></span><div><br></div><div><br></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 30, 2015 at 9:23 PM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</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">Hi Namchul,<div class="gmail_extra"><br></div><div class="gmail_extra">Please take all of this with a pinch of salt; mappings between Ensembl and RefSeq transcripts vary in quality, and there is no guarantee that if a corresponding ID is found it will have the same transcript sequence (typically they will differ in non-coding regions but coding differences are also not uncommon).</div><div class="gmail_extra"><br></div><div class="gmail_extra">Any sequence differences will therefore make values calculated against Ensembl transcripts (such as those in dbNSFP) potentially invalid and misleading. Also bear in mind that the current dbNSFP release may use transcripts from an older version of Ensembl than is current for the VEP.</div><div class="gmail_extra"><br><div class="gmail_quote"><span class="">On 30 April 2015 at 08:46, namchul ghim <span dir="ltr"><<a href="mailto:chulghim@gmail.com" target="_blank">chulghim@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Thanks.. <div><br></div><div>1) </div><div> I got grch39 mapping list (ensembl transcriptid and refseq_transcript id) from your homo_sapiens_core_79_38</div><div><br></div><div>But, I can't homo_sapiens_core_79_37 database. </div><div>where do i get GRCh37 version's mapping list ?</div></div></blockquote><div><br></div></span><div>You can connect to the 37 database on port 3337:</div><div><br></div><div>mysql -<a href="http://hensembldb.ensembl.org" target="_blank">hensembldb.ensembl.org</a> -uanonymous -P3337 -Dhomo_sapiens_core_79_37</div><div><br></div><div>You could also try BioMart to retrieve the mapping, e.g:<br></div><div><br></div><div><a href="http://grch37.ensembl.org/biomart/martview/b7985fa1a36be3b616c0b915031b9a1a" target="_blank">http://grch37.ensembl.org/biomart/martview/b7985fa1a36be3b616c0b915031b9a1a</a><br></div><span class=""><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><br></div><div><br></div><div>2) I will insert refseq id in dbNSFP db file. <br></div><div> What is the field name ?</div></div></blockquote><div><br></div></span><div>The field VEP uses in the dbNSFP file is named Ensembl_transcriptid. You could replace this with the RefSeq ID and use the plugin unmodified, but it would be better to add it as a new field and modify the plugin (just grep dbNSFP.pm for Ensembl_transcriptid to see where you need to change it).</div><div> </div><div>Regards</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Will</div></font></span><div><div class="h5"><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div> </div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Apr 29, 2015 at 7:27 PM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi Namchul,<div><br></div><div>The current version of the dbNSFP plugin does not work with the RefSeq cache; this is because data is looked up on a key constructed from the position, variant allele and Ensembl transcript ID, so will not work when the input key contains the RefSeq transcript ID and not the Ensembl one.</div><div><br></div><div>If dbNSFP add the RefSeq transcript ID as a field in the data files, then the plugin could use this as its key; until then the plugin will only work with the Ensembl cache.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On 29 April 2015 at 02:38, namchul ghim <span dir="ltr"><<a href="mailto:chulghim@gmail.com" target="_blank">chulghim@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div><div dir="ltr"><div>my environment</div><div> release v79 <br></div><div> latest vep </div><div> dbnsfp version - 2.9</div><div> reference - grch37</div><div> </div><div>dbNSFP plugin works at vep original cache version very well.</div><div>but, does not work at refseq cache version..</div><div><br></div><div>Why?</div><div>my command is the following. </div><div><br></div><div>perl /src/ensembl-tools/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i example_GRCh37.vcf --cache --offline --everything --force_overwrite --dir /cache/GRCh37 -o out.vcf --vcf --refseq --species homo_sapiens --xref_refseq --regulatory --flag_pick_allele --buffer_size 5000 --fork 10 --hgvs --force --fasta /cache/GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --plugin dbNSFP,/cache/GRCh37/dbNSFP/dbNSFP.gz,ref,alt,aaref,aaalt,rs_dbSNP141,hg38_chr,hg38_pos,genename,Uniprot_acc,Uniprot_id,Uniprot_aapos,Interpro_domain,cds_strand,refcodon,SLR_test_statistic,codonpos,fold-degenerate,Ancestral_allele,Ensembl_geneid,Ensembl_transcriptid,aapos,aapos_SIFT,aapos_FATHMM,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,LRT_score,LRT_converted_rankscore,LRT_pred,MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,MutationAssessor_score,MutationAssessor_rankscore,MutationAssessor_pred,FATHMM_score,FATHMM_rankscore,FATHMM_pred,MetaSVM_score,MetaSVM_rankscore,MetaSVM_pred,MetaLR_score,MetaLR_rankscore,MetaLR_pred,Reliability_index,PROVEAN_score,PROVEAN_converted_rankscore,PROVEAN_pred,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP46way_primate,phyloP46way_primate_rankscore,phyloP46way_placental,phyloP46way_placental_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phastCons46way_primate,phastCons46way_primate_rankscore,phastCons46way_placental,phastCons46way_placental_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,SiPhy_29way_pi,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,LRT_Omega,UniSNP_ids,1000Gp1_AC,1000Gp1_AF,1000Gp1_AFR_AC,1000Gp1_AFR_AF,1000Gp1_EUR_AC,1000Gp1_EUR_AF,1000Gp1_AMR_AC,1000Gp1_AMR_AF,1000Gp1_ASN_AC,1000Gp1_ASN_AF,ESP6500_AA_AF,ESP6500_EA_AF,ARIC5606_AA_AC,ARIC5606_AA_AF,ARIC5606_EA_AC,ARIC5606_EA_AF,ExAC_AC,ExAC_AF,ExAC_Adj_AC,ExAC_Adj_AF,ExAC_AFR_AC,ExAC_AFR_AF,ExAC_AMR_AC,ExAC_AMR_AF,ExAC_EAS_AC,ExAC_EAS_AF,ExAC_FIN_AC,ExAC_FIN_AF,ExAC_NFE_AC,ExAC_NFE_AF,ExAC_SAS_AC,ExAC_SAS_AF,clinvar_rs,clinvar_clnsig,clinvar_trait,COSMIC_ID,COSMIC_CNT<br></div><div><br></div><div><br></div><div><br></div></div>
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