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From: Maira b. <mai...@ir...> - 2018-10-24 12:44:58
|
Hello, The database for rice7 is not available on version 4.3. It was available on version 4.2, how can we access this file ? When trying to download it, I get this error : ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_rice7.zip java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at org.snpeff.util.Download.download(Download.java:178) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:32) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:86) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72) at org.snpeff.SnpEff.run(SnpEff.java:1041) at org.snpeff.SnpEff.main(SnpEff.java:159) Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at org.snpeff.util.Download.download(Download.java:127) |
From: Choudhari, S. <su...@pu...> - 2016-06-24 13:13:28
|
Hi! I am trying to annotate the SNPs for maize samples using snpEff. In the annotation column or the EFF column in the result vcf file some positions are annotated as "NA". But these positions are actually present in the gff file with some gene feature. See example below: For gene GRMZM2G027219: CHROM POS EFF 2 74716293 NA The same position falls between an exon in the gff file from which the database is built. Exon 74716207 74716341 five_prime_UTR 74716207 74716797 My question is why this positon is annotated as NA and not exon or 5' as shown in the gff file. There are several other positons that are annotated as NA thought these positions are present in the gff file. Please if you could explain me in what condition a position will be annotated as "NA". Thanks! |
From: Jean-Paul B. <jea...@av...> - 2016-06-21 10:45:10
|
Hello, snpEff_latest_core.zip corresponds now with the version 4.3 of SnpEff. Today only a few SnpEff databases are available with this new version and the command 'download' doesn't find the requested file in http://downloads.sourceforge.net/project/snpeff/databases/v4_3. Is it possible to load files from http://downloads.sourceforge.net/project/snpeff/databases/v4_2 with the version 4.3 of SnpEff ? Are the databases prepared for the version 4.2 of SnpEff compatible with this version 4.3 ? Best regards, Jean-Paul Bouchet Institut National de la Recherche Agronomique - Centre de Provence, Alpes, Côte d'Azur UR 1052 <http://w3.avignon.inra.fr/gafl/en> - Génétique et Amélioration des Fruits et Légumes Domaine Saint-Maurice - CS 60094 - F-84143 Montfavet cedex - France |
From: Jolly S. <jol...@gm...> - 2016-01-13 22:56:28
|
Hello All, I am working with a plant pathogen Phytophthora infestans and trying to annotate SNPs/INDELs found by GATK. I gave the following command to find if there is a database for P.infestans. java -jar /opt/linux/centos/7.x/x86_64/pkgs/snpEff/4.1K/snpEff.jar databases | grep -i infestans which gave me ASM14294v1.27 http://downloads.sourceforge.net/project/snpeff/databases/v4_1/snpEff_v4_1_ASM14294v1.27.zip however when I tried to use the above database I got the error: java -Xmx3g -jar snpEff.jar -c snpEff.config ASM14294v1.27 total_SNPs_INDELS.GATK.vcf 00:00:00.000 ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_1/snpEff_v4_1_ASM14294v1.27.zip java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at ca.mcgill.mcb.pcingola.util.Download.download(Download.java:147) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:31) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:85) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:71) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:942) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadDb(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:938) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:921) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:905) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:128) Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at ca.mcgill.mcb.pcingola.util.Download.download(Download.java:96) ... 9 more java.lang.RuntimeException: Genome download failed! at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadDb(SnpEff.java:321) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:938) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:921) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:905) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:128) How can I use the database when it is not present in the current folder. Please help me out. Thanks -- Jolly Shrivastava Ph.D candidate (Genetics, Genomics and Bioinformatics) University of California, Riverside |
From: Eric G. <shi...@gm...> - 2015-10-19 21:44:22
|
I had run it and deffinitely looks that is not B73 RefGen_v3, are you planing to add v3? is better if I do my database? Thank you very much Regards 2015-10-19 15:35 GMT-05:00 Eric González <shi...@gm...>: > Hi > > I am new using snpEff, I would like to use it to study maize, but I am not > sure about which version of the reference genome of maize you use for your > database. > > I use: > > java -jar /home/shinken/bin/snpEff/snpEff.jar databases | grep -i maize > > And that give me: > > maizeZmB73 > Maize_ZmB73_5b > > http://downloads.sourceforge.net/project/snpeff/databases/v4_1/snpEff_v4_1_maizeZmB73.zip > testMaizeZmB73 Test > MaizeZmB73 > > http://downloads.sourceforge.net/project/snpeff/databases/v4_1/snpEff_v4_1_testMaizeZmB73.zip > > But I am still not sure about which reference genome you use: > *The current Reference Genome for Maize is B73 RefGen_v3*. > > At maize GDB (http://www.maizegdb.org/assembly) there is this information: > > gene model set description assembly version 5a Working Gene Set (WGS) > RefGen_v2 5b Filtered Gene Set (FGS) - subset of WGS RefGen_v2 5b+ Filtered > Gene Set, mostly projections of 5b RefGen_v3 > > > > > > > > Thus you use version 2? > > Thanks > > > -- > Eric > -- Eric |
From: Eric G. <shi...@gm...> - 2015-10-19 20:35:26
|
Hi I am new using snpEff, I would like to use it to study maize, but I am not sure about which version of the reference genome of maize you use for your database. I use: java -jar /home/shinken/bin/snpEff/snpEff.jar databases | grep -i maize And that give me: maizeZmB73 Maize_ZmB73_5b http://downloads.sourceforge.net/project/snpeff/databases/v4_1/snpEff_v4_1_maizeZmB73.zip testMaizeZmB73 Test MaizeZmB73 http://downloads.sourceforge.net/project/snpeff/databases/v4_1/snpEff_v4_1_testMaizeZmB73.zip But I am still not sure about which reference genome you use: *The current Reference Genome for Maize is B73 RefGen_v3*. At maize GDB (http://www.maizegdb.org/assembly) there is this information: gene model set description assembly version 5a Working Gene Set (WGS) RefGen_v2 5b Filtered Gene Set (FGS) - subset of WGS RefGen_v2 5b+ Filtered Gene Set, mostly projections of 5b RefGen_v3 Thus you use version 2? Thanks -- Eric |
From: Rocky S. - X. <roc...@xc...> - 2013-06-18 09:37:21
|
Dear Concern, I have been using snpeff for rice genome variant call annotation. It runs well and the annotation output is easy to classify for region based. I would also like to annotate variants call from castor bean scientific name Ricinus communis but I could not find castor bean database at your snpeff site. Could you please tell how could I annotate for this genome. -------------- With regards, Rocky Singh Scientist Xcelris Genomics, Old Premchand nagar road, Opp. Satyagrah chavani, Bodakdev, Ahmedabad - 380054 Tel: +91-79-66197777 Email: roc...@xc... www.xcelrisgenomics.com "Please don't print this e-mail unless you really need to. Save Paper, Save Trees" -------------------------------------------------------------------------------- Disclaimer The information contained in this e-mail message and / or attachments to it may contain confidential or privileged information of Xcelris Labs Limited and / or its group companies. If you are not the intended recipient, any dissemination, use, review, distribution, printing or copying of the information contained in this e-mail message and / or attachments to it is strictly prohibited. If you have received this communication in error, please notify us by reply e-mail or telephone and immediately delete / destroy the message and / or any attachments permanently. Any views or opinions presented in this e-mail are solely those of the author and do not necessarily represent those of the company. Employees of the company are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by e-mail communication. Any such communication is contrary to company policy and outside the scope of the employment of the individual concerned. The company will not accept any liability in respect of such communication. No employee or associate is authorized to conclude any binding agreement on behalf of Xcelris with another party by e-mail without expressly written confirmation of the company. Warning-Computer viruses can be transmitted via e-mail. The recipient should check this e-mail and any attachment for the presence of viruses. The company has taken every reasonable precaution to minimize this risk, and is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before acting upon the e-mail or any attachment to it. -------------------------------------------------------------------------------- |
From: Pablo C. <pci...@ta...> - 2013-01-09 23:34:09
|
test |