bulkdownload fastq files from ENA

Hi,

I want to download fastq files from this study. Tried pysradb, pysradb download -p SRP165962 --out-dirbut it downloads all empty folders anonftp@ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR806/SRR8068516/SRR8068516.sra

Any better way to download the data?

Kindly suggest

fastq ena

• 2,252 views • link

updated 3.4 years ago by Ram

• written 6.3 years ago by amitpande74 •

1 answer

Use sra-explorer: sra-explorer : find SRA and FastQ download URLs in a couple of clicks You can get bulk download command lines.

• 0 views • link

written 6.3 years ago by GenoMax

If I want to directly download this in an external hard drive ?

• 0 views • link

written 6.3 years ago by amitpande74 •

Set the destination to the desired location.

• 0 views • link

written 6.3 years ago by GenoMax

More posts like this

Aspera ascp Command Fails with "Failed to open TCP connection for SSH" Error
written 2.0 years ago by Akansh •

Hello Biostars community, I'm encountering an issue while attempting to download a file using the Aspera ascp command. Here’s the command I’m using: "ascp -QT …
SRA ftp site change?
written 5.9 years ago by michael.j.apostolides •

Hi all, I used to be able to download .sra files from SRA in the following way: $ nohup wget -c ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR165/SRR1657561/SRR1657561.sra However, now it …
Problem while downloading SRR file via **ASPERA CONNECT**
written 6.4 years ago by dpc

I was trying to download SRR data (**SRR304976**) using aspera connect. I have used the following command: /home/deep/.aspera/connect/bin/ascp -T -k1 -i /home/deep/.aspera/connect/etc/asperaweb_id_dsa.openssh anonftp@ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR304/SRR304976/SRR304976.sra /home/deep/XXXXXXX BUT, …
download the file of SRR from ftp
written 6.4 years ago by yueli7

Hello, I want to wget the file of `SRR10586524`. I tried following websit, but I have no idea. Thanks in advance for any help! Best, …
i can't find the SRR sample on NCBI FTP, such as SRR018260
written 7.1 years ago by zhao03 •

I used FTP to search SRR018260 that i want to download, however, SRR018260 sample can't be found. is the website error? or i should download …
i have some problems in using aspera to download sra
written 9.6 years ago by shiisgood •

Hello,dear everyone. I want to download some RNA-seq raw data from NCBI by using Aspera. i used the command ~/.aspera/connect/bin/ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -k 0 -T …
Downloaing SRA using Aspera
written 10.0 years ago by always_learning

Dear Bioinformaticians, I was trying to download some data from SRS using Aspera. I was able to download this example SRR304976 mentioned at http://www.ncbi.nlm.nih.gov/books/NBK158899/ sample …
downloading fasta or fastq format with aspera
written 11.2 years ago by zizigolu

hey there, I installed aspera to transfer data from NCBI, for example this link starting to download a sra file... http://www.ncbi.nlm.nih.gov/public/?/ftp/sra/sra-instant/reads/ByRun/sra/SRR/SRR292/SRR292241 If I need fasta …
Download Geo Sra Data Using Aspera Connect
written 13.5 years ago by dfernan

I'd like to download the following SRA files: <a href='ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP014/SRP014751'>ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP014%2FSRP014751</a> using aspera connect in our university linux cluster but when I try ascp'ing it asks …
How To Retrieve A .Fastaq File From Sra Using Wget? (And Not Aspera)
written 15.5 years ago by Marina Manrique

Hi! I'd like to download a .sra file containing the fastq files for an experiment in the SRA using the wget command. I've been looking …