Downloading data from Short Read Archive

Question

[biomagician]

Dear all,

Does anyone know how I can download data from this page on Short Reach Archive?

https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRX1728385

Thanks.

C.

Answer 1

[Michael]

Simply use SRA tools: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3452286

[biomagician]

Thanks it worked!

Answer 2

[EagleEye]

1) Download and install SRAtoolkit

2) Use fastq-dump to download SRA files as fastq files, (in your case SRR or run id is SRR3452286 )

fastq-dump --split-3 SRR3452286

[biomagician]

Thanks it worked! What's --split-3 for? I can't find it in the documentation. https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump The closest is --split-spot

[EagleEye]

Here is the answer in previously discussed post.