downloading many sra files for single cell analysis
I'm trying to download ~ 1000 sra files for single cell data. I tried getting the SRA run info to then download all the SRA files from there, but it's taking a really long time. What is the fastest way to download so many files at once from the same BioProject? I don't typically work with single cell data, so please excuse my ignorance if the answer is obvious!
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Satyajeet Khare
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bioinfgeekgirl •
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bioinfgeekgirl •
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You can use ftp
wget -P ../fastq $url
And generate url based on SRR id using a for-loop. Where URL can be from GEO, EBI or DDBJ.
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I usually use aspera which typically is faster than ftp. Make use of gnu parallel to convert sra to fastq, or even during downloading if you really have good net speed.
P.S. There is bechmark here for reference.