Entering edit mode
Jack Zhu
▴
170
@jack-zhu-3338
Last seen 7.0 years ago
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BTW, "SRA049463" is in 'unpublished' status.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
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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out of date because the submission dates are often relatively old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