Forum:Download manager for SRA
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10.0 years ago
Biojl ★ 1.7k

Hi,

I was wondering what people is using to download huge amounts of experiments in SRA format. I'm currently using a home made script that downloads everything and classifies it using the runinfo table that can be downloaded from the sra selector (http://www.ncbi.nlm.nih.gov/Traces/study/?go=home)

I find this extremely cumbersome but is the best option I got. Is there any download manager I'm missing? What do you people use to download a (big) set of experiments.

ncbi SRA RNA-Seq • 2.8k views
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2
Entering edit mode
10.0 years ago

Well I start with something like this

esearch \
  -db sra \
  -query PRJNA40075 | \
  efetch \
  --format runinfo | \
  cut -d ',' -f 1 | \
  grep SRR | \
  head -5 | \
  xargs fastq-dump -X 10 --split-files

Also seen here: How to download raw sequence data from GEO/SRA

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If you plan to use BWA mem make sure to set the --origfmt flag for the fasts-dump Aligning paired end fastq files dumped from SRA

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never ran into this myself - though I do download/process paired end reads - there is probably more to it, perhaps the way the sra file was built.

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10.0 years ago

Maybe the SRAdb package from R/Bioconductor can help? As mentioned in, e.g. this A: SRX from SRR IDs . It will help deciding what needs to be downloaded.

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