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Question: download SRR*.lite.sra files using fastq-dump command
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gravatar for xhe764
14 months ago by
xhe7640
xhe7640 wrote:

I'm trying to download some chip-seq datasets from NCBI Gene Expression Omnibus using fastq-dump command like

fastq-dump SRR499718.lite.sra 

and I got error message like below:

2016-09-27T16:33:36 fastq-dump.2.7 err: item not found while constructing within virtual database module - the path 'SRR499718.lite.sra' cannot be opened as database or table.

However, running the command like following

fastq-dump SRR499718

worked fine.

When checking the GEO or SRA websites, I couldn't find any files with extension .lite.sra. My questions are 1) what are the differences between SRR*.lite.sra file and SRR*.sra file? 2) where can I download files with the extension .lite.sra? 

Any suggestions will be highly appreciated.

By the way, the problem rose when I was practising the following chip-seq workflow: 

source("http://bioconductor.org/workflows.R")
workflowInstall("chipseqDB")
sra.numbers <- c("SRR499718", "SRR499719", "SRR499720", "SRR499721", 
    "SRR499734", "SRR499735", "SRR499736", "SRR499737", "SRR499738")
grouping <- c("proB-8113", "proB-8113", "proB-8108", "proB-8108", 
    "matureB-8059", "matureB-8059", "matureB-8059", "matureB-8059", "matureB-8086")
all.sra <- paste0(sra.numbers, ".lite.sra")
data.frame(SRA=all.sra, Condition=grouping)
for (sra in all.sra) {
    code <- system(paste("fastq-dump", sra))
    stopifnot(code==0L)
}

After the for loop, I got the same error message as shown above.

 

ADD COMMENTlink modified 13 months ago by James W. MacDonald45k • written 14 months ago by xhe7640
0
gravatar for James W. MacDonald
13 months ago by
United States
James W. MacDonald45k wrote:

I think the lite.sra files have been phased out, so you need to do

for (sra in all.sra) {
    code <- system(paste("fastq-dump", sra.numbers))
    stopifnot(code==0L)
}

instead.

ADD COMMENTlink written 13 months ago by James W. MacDonald45k

Thank you so much. This explains everything.

ADD REPLYlink written 13 months ago by xhe7640

I would also point out that using Aspera to download is really the way to go, and using fastq-dump directly is probably much slower than using prefetch first (which will use Aspera if installed correctly) and then using fastq-dump to convert.

ADD REPLYlink written 13 months ago by James W. MacDonald45k
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