Question: download from SRA
0
gravatar for zh.khodadadi
12 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 • 602 views
ADD COMMENTlink modified 12 months ago by st.ph.n1.6k • written 12 months ago by zh.khodadadi0
0
gravatar for Mike
12 months ago by
Mike730
UK
Mike730 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 12 months ago by Mike730
0
gravatar for Satyajeet Khare
12 months ago by
Satyajeet Khare1000
Pune, India
Satyajeet Khare1000 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 12 months ago • written 12 months ago by Satyajeet Khare1000

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

ADD REPLYlink written 12 months ago by st.ph.n1.6k

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 12 months ago • written 12 months ago by Satyajeet Khare1000
0
gravatar for st.ph.n
12 months ago by
st.ph.n1.6k
Philadelphia, PA
st.ph.n1.6k 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 12 months ago • written 12 months ago by st.ph.n1.6k
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