User: Jack Zhu

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Jack Zhu160
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Posts by Jack Zhu

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Error downloading using SRAdb
... Hi, It looks ERR1021452 does not have an entry in the fastq download site:   ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR102 ----------------- > sraConvert (c("ERR1021452"), out_type = c("sra", "submission", "study", "sample", "experiment", "run"), sra_con)          run submission     study    samp ...
written 12 months ago by Jack Zhu160
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Comment: C: error in SRAdb
... Hi Robert and Dan, Out server was down during the weekend and it looks Dropbox has blocked downloading files programmatically. Anyway our server is back. Please try again. Sorry for the inconvenience. Jack ---- Yuelin Jack Zhu Biologist (Bioinformatics) Genetics Branch/CCR/NCI/NIH Tel: (301)496 ...
written 2.7 years ago by Jack Zhu160
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Comment: C: SRAmetadb Bioconductor package; study record count low for 2013
... Hi Jamie and all, By modifying my codes and pulling data from a curated table (SRA_Accessions.tab) from the SRA, I think the missing 'submission_date' in the submission table have been fixed: strftime('%Y', s.submission_date) count(*) 1 2008 348 2 ...
written 2.8 years ago by Jack Zhu160
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Answer: A: SRAmetadb Bioconductor package; study record count low for 2013
... Hi all, Regarding missing studies by submission_date for 2013 and 2014 in the SRAdb SQLite database, I did some investigation and found the reason. The metadata in the SRAdb is mainly parsed from the XML files of the SRA submissions and it is true with the submission table. But I see quite some su ...
written 2.8 years ago by Jack Zhu160
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SRAdb package - problems
... Hi Preethy, It looks like you are running a old version of SRAdb, which might be problematic since both NCBI SRA and EBI ERA has had some changes and the functions in SRAdb have been updated accordingly. The following is my test with correct commands in newer version of SRAdb: ------------------- ...
genetics sradb written 3.8 years ago by Jack Zhu160
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getGEO vs GEOmetadb
... Hi Thomas, Sorry that I missed your posts on the bioconductor mailing list. We did have issues with updating recent GEO data and that seem has been fixed: ----------------------- > con <- dbConnect(SQLite(), "GEOmetadb.sqlite") > dat <- dbGetQuery(con, "select * from gds where gds = 'G ...
lung homo sapiens pseudomonas aeruginosa geometadb written 3.8 years ago by Jack Zhu160
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SRAdb: is the database missing some entries? (Ben Woodcroft)
... 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 stud ...
sradb written 4.8 years ago by Jack Zhu160 • updated 4.8 years ago by Ben Woodcroft40
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[Bioc-sig-seq] SRAdb and getFastq
... Hi Kirti, As Martin said, in the newer version of BioC (both 2.7 release and 2.8 dev version), there were changes to reflect the NCBI removal of fastq files: 1. Removed functions of listFastq, getFastqInfo and getFaastq 2. Added functions of listSRAfile, getSRAinfo and getSRAfile 3. Modi ...
cancer convert written 6.1 years ago by Jack Zhu160
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Bioconductor Digest, Vol 95, Issue 7
... Hi Mark and Sean, As Sean mentioned, the NCBI SRA group removed fastq data files from their ftp site, but supplies sra or sra-lite data files for downloading. In order to deal with this significant changes, I have modified the SRA package (in both 2.7 release and dev version): 1. Removed functio ...
process sradb written 6.2 years ago by Jack Zhu160
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Comment: C: 'SRAdb useful for visualizing BAM files'
... Hi Aaron, Maybe there is need for serving BAM files for NCBI SRA runs somewhere. It seems that that will take a consortium to do it in terms of work and standards. I guess large consumers of public Next-Gen Sequencing data should lead this. Jack On Mon, Apr 12, 2010 at 9:32 AM, Aaron Mackey w ...
written 7.0 years ago by Jack Zhu160

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