Question: download from SRA
0
gravatar for zh.khodadadi
14 months ago by
zh.khodadadi0 wrote:

how can i download a list of SRR accession from SRA by sratoolkit? what is the configuration list of SRR numbers?

rna-seq • 748 views
ADD COMMENTlink modified 14 months ago by st.ph.n1.9k • written 14 months ago by zh.khodadadi0
2
gravatar for st.ph.n
14 months ago by
st.ph.n1.9k
Philadelphia, PA
st.ph.n1.9k wrote:

Throw your SRR numbers into a file called SRR_list.txt, one number per line.

Then add this to a file called get_SRR_data.sh

   #!/usr/bin/bash

    fastq-dump --split-3 $1

and run on the command line with:

cat SRR_list.txt | xargs -n 1 bash get_SRR_data.sh

Fastq-dump will pull the data, one by one for all accesion numbers in your list, and turn each into a fastq at the same time. The --split-3 will create paired end files if available. Provide the path to fastq-dump in the bash script, if it is not installed globally on your system.

If you prefer @Satya's suggestion of using wget:

#!/usr/bin/bash

wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/"$1"/"$1".sra

fastq-dump --split-3 "$1".sra
ADD COMMENTlink modified 14 months ago • written 14 months ago by st.ph.n1.9k
0
gravatar for Mike
14 months ago by
Mike880
UK
Mike880 wrote:

have a look at @Obi Griffith previous post:

Determine the SRR number and then download the data at the command-line with:

prefetch -v SRR925811

How to download raw sequence data from GEO/SRA

ADD COMMENTlink written 14 months ago by Mike880
0
gravatar for Satyajeet Khare
14 months ago by
Satyajeet Khare1.1k
Pune, India
Satyajeet Khare1.1k wrote:

I use wget to download

wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR(first three digits)/SRR(all digits)/SRR(all digits).sra

and fastq-dump to convert to fastq

fastq-dump --split-3 SRR(all digits).sra
ADD COMMENTlink modified 14 months ago • written 14 months ago by Satyajeet Khare1.1k

There's no need to pull the data, and then convert to fastq. fastq-dump will do both for you.

ADD REPLYlink written 14 months ago by st.ph.n1.9k

I agree, but wget with ftp is way faster, unless there is a way to use fastq-dump with ftp that I am not aware of.

ADD REPLYlink modified 14 months ago • written 14 months ago by Satyajeet Khare1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 599 users visited in the last hour