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Question: SRAdb: is the database missing some entries? (Ben Woodcroft)
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gravatar for Jack Zhu
5.4 years ago by
Jack Zhu170
Jack Zhu170 wrote:
Hi Ben and all, Sorry for late response - just came back from a vacation. I found the problem - our newest SRAdb SQLite file was not copied to the web server due to permission issue. I have fixed it: > sraConvert(c('SRA036600','SRA049463','ERA062401'), sra_con= sra_con) submission study sample experiment run 1 ERA062401 ERP000941 ERS066098 ERX024719 ERR047656 2 ERA062401 ERP000941 ERS066098 ERX024722 ERR047659 3 ERA062401 ERP000941 ERS066097 ERX024712 ERR047649 4 ERA062401 ERP000941 ERS066097 ERX024710 ERR047647 5 ERA062401 ERP000941 ERS066098 ERX024721 ERR047658 6 ERA062401 ERP000941 ERS066097 ERX024711 ERR047648 7 ERA062401 ERP000941 ERS066097 ERX024708 ERR047645 8 ERA062401 ERP000941 ERS066097 ERX024715 ERR047652 9 ERA062401 ERP000941 ERS066098 ERX024720 ERR047657 10 ERA062401 ERP000941 ERS066097 ERX024713 ERR047650 11 ERA062401 ERP000941 ERS066097 ERX024709 ERR047646 12 ERA062401 ERP000941 ERS066098 ERX024723 ERR047660 13 ERA062401 ERP000941 ERS066098 ERX024717 ERR047654 14 ERA062401 ERP000941 ERS066097 ERX024714 ERR047651 15 ERA062401 ERP000941 ERS066098 ERX024718 ERR047655 16 ERA062401 ERP000941 ERS066098 ERX024716 ERR047653 17 SRA036600 SRP006780 SRS193106 SRX062801 SRR205889 BTW, "SRA049463" is in 'unpublished' status. Thanks for your message. Your comments will be highly appreciated. Jack --------------------------------------------------------------------- Hi, Firstly thanks to the creators of this very useful package. I've come across SRA identifiers that don't appear to be in the database (a minority, but still). Here's a few: SRA036600 DRX001436 SRA049463 ERA062401 ERA062401 For example: > library(SRAdb) > sra_con = dbConnect(SQLite(),'SRAmetadb.sqlite') > sraConvert(c('SRA036600'), sra_con= sra_con) [1] submission study sample experiment run <0 rows> (or 0-length row.names) However this isn't a bogus accession because I can see it on the NCBI SRA website. I could be wrong but I don't think it is as simple as the metadata being out of date because the submission dates are often relatively old (SRA036600 was 2011-05-13) and there's metadata from more recent SRA submissions in the SRAdb). Any ideas? Thanks in advance, ben
ADD COMMENTlink modified 5.4 years ago by Ben Woodcroft40 • written 5.4 years ago by Jack Zhu170
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gravatar for Ben Woodcroft
5.4 years ago by
Ben Woodcroft40 wrote:
Hi Jack, Thanks for the reply and fix - you had me worried! I have big plans for this database. It seems to find data for all those that were missing (my total list is 52 accessions), except for SRA023700 - maybe this particular one was only recently released? Is there any way to tell? I notice you've also deleted not publicly available data from the database, I note, which seems like a good thing. Thanks, ben Date: Wed, 20 Jun 2012 17:30:22 -0400 From: Jack Zhu <zhujack@mail.nih.gov> > > Hi Ben and all, > > Sorry for late response - just came back from a vacation. I found the > problem - our newest SRAdb SQLite file was not copied to the web > server due to permission issue. I have fixed it: > > > sraConvert(c('SRA036600','SRA049463','ERA062401'), sra_con= sra_con) > submission study sample experiment run > 1 ERA062401 ERP000941 ERS066098 ERX024719 ERR047656 > 2 ERA062401 ERP000941 ERS066098 ERX024722 ERR047659 > 3 ERA062401 ERP000941 ERS066097 ERX024712 ERR047649 > 4 ERA062401 ERP000941 ERS066097 ERX024710 ERR047647 > 5 ERA062401 ERP000941 ERS066098 ERX024721 ERR047658 > 6 ERA062401 ERP000941 ERS066097 ERX024711 ERR047648 > 7 ERA062401 ERP000941 ERS066097 ERX024708 ERR047645 > 8 ERA062401 ERP000941 ERS066097 ERX024715 ERR047652 > 9 ERA062401 ERP000941 ERS066098 ERX024720 ERR047657 > 10 ERA062401 ERP000941 ERS066097 ERX024713 ERR047650 > 11 ERA062401 ERP000941 ERS066097 ERX024709 ERR047646 > 12 ERA062401 ERP000941 ERS066098 ERX024723 ERR047660 > 13 ERA062401 ERP000941 ERS066098 ERX024717 ERR047654 > 14 ERA062401 ERP000941 ERS066097 ERX024714 ERR047651 > 15 ERA062401 ERP000941 ERS066098 ERX024718 ERR047655 > 16 ERA062401 ERP000941 ERS066098 ERX024716 ERR047653 > 17 SRA036600 SRP006780 SRS193106 SRX062801 SRR205889 > > BTW, "SRA049463" is in 'unpublished' status. > > Thanks for your message. Your comments will be highly appreciated. > > Jack > -- -- Ben Woodcroft http://ecogenomic.org/users/ben-woodcroft <http: www.ecogenomic.org=""/> [[alternative HTML version deleted]]
ADD COMMENTlink written 5.4 years ago by Ben Woodcroft40
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