Question: download from SRA
1
gravatar for zh.khodadadi
21 months ago by
zh.khodadadi10
zh.khodadadi10 wrote:

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

rna-seq • 1.6k views
ADD COMMENTlink modified 5 weeks ago by Federico Giorgi390 • written 21 months ago by zh.khodadadi10

Did you read the tutorial?

How to download raw sequence data from GEO/SRA

ADD REPLYlink written 5 weeks ago by YaGalbi1.3k
2
gravatar for st.ph.n
21 months ago by
st.ph.n2.2k
Philadelphia, PA
st.ph.n2.2k 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 21 months ago • written 21 months ago by st.ph.n2.2k
0
gravatar for Mike
21 months ago by
Mike980
UK
Mike980 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 21 months ago by Mike980
0
gravatar for Satyajeet Khare
21 months ago by
Satyajeet Khare1.2k
Pune, India
Satyajeet Khare1.2k 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 21 months ago • written 21 months ago by Satyajeet Khare1.2k

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

ADD REPLYlink written 21 months ago by st.ph.n2.2k

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 21 months ago • written 21 months ago by Satyajeet Khare1.2k

As far as I know, sra can block the ip if you download a lot of files with wget.

ADD REPLYlink written 5 weeks ago by grant.hovhannisyan880

In my experience, the fastest and the most secure (without connection interruptions) is to use prefetch with aspera, then convert sra files to fastq with fastq-dump. The whole thing saves a lot of time.

ADD REPLYlink written 5 weeks ago by grant.hovhannisyan880
0
gravatar for Federico Giorgi
5 weeks ago by
Columbia University
Federico Giorgi390 wrote:

You can use xargs and the sra-toolkit prefetch to download every SRR id contained in a txt file list, like:

xargs -n1 prefetch < SRR_Acc_List.txt
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Federico Giorgi390
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: 1360 users visited in the last hour