Question: downloading many sra files for single cell analysis
0
gravatar for bioinfgeekgirl
24 months ago by
bioinfgeekgirl0 wrote:

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!

sra • 1000 views
ADD COMMENTlink modified 24 months ago by Satyajeet Khare1.3k • written 24 months ago by bioinfgeekgirl0
1

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.

ADD REPLYlink modified 24 months ago • written 24 months ago by eldronzhou350
0
gravatar for Satyajeet Khare
24 months ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k wrote:

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.

ADD COMMENTlink modified 24 months ago • written 24 months ago by Satyajeet Khare1.3k
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