download data problem

Question

[evelyn]

Hello, I want to download sequence files from NCBI FTP SRA. I am not sure how to find a ftp hyperlink for the file location from NCBI.

Answer 1

[GenoMax]

Use sra-explorer tool from Phil Ewels: sra-explorer : find SRA and FastQ download URLs in a couple of clicks

Take a look at example screenshots I have posted in that thread.

[evelyn]

@genomax, thank you! I tried the ftp link from sra-explorer into linux array to download a batch of files but gave an error that No such file exists.

[ATpoint]

Please show relevant code.

[evelyn]

Hello, I want to download many files using array from ftp. But I checked the ftp link for an individual file manually and it seems the directory is empty. Is there any other way to access the ftp files?

[ATpoint]

Details please!!! Which ftp site, which samples??

[ATpoint]

Also: Fast download of FASTQ files from the European Nucleotide Archive (ENA)

[evelyn]

For a list of files I am using this array on linux:

lines=$(wc -l input.txt|cut -f 1 -d ' ')
for i in $(eval echo {1..$lines}); do
name=$(head -n $i  input.txt|tail -n 1 |cut -f 1)
var1=$(head -n $i  input.txt|tail -n 1 |cut -f 2)
var2=$(head -n $i  input.txt|tail -n 1 |cut -f 3)
input=$(echo ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX239/$var1/$var2/$var2.sra)
wget -I $input -O $name
done

Thank you for your help!

[ATpoint]

This is overly complicated. Why not just getting the download links provided by sra-explorer?

Answer 2

[tothepoint]

May be this help: Download SRA file

High speed download SRA files..