How to download raw data in batch from NCBI based on Series Accession number or Platform ID

Question

[biolab]

Dear all,

I have a list of NCBI GEO Series Accession numbers and Platform IDs, and want to download the raw data in batch. A previous post on Biostars presents a good example of batch download (How to download raw sequence data from GEO/SRA ), but that solution is based on project ID rather than GEO Series Accession number. Does anyone know how to work out this task? Thank you very much!

[GenoMax]

Can you post an example of the Accession number you are interested in? @Istvan's solution with eUtils should be able to accommodate your needs.

[biolab]

Thank you for your comment, genomax! The GEO Series Accession Number is something like GSE65022, and the Platform ID is like GPL19657. I want to get the SRA number something like SRR4024915.

[Buffo]

This may be helpul batchentrez

[biolab]

Hi, Buffo, thanks for your comment! However, after uploading a list of Platform ID (eg, GPL19657), I could not get the SAR run number, which is something like SRR4024915.

[microfuge]

Hi, Just in case you are only interested in SRR ids, SRA run selector is a very good option. You can either enter GSE65022 in the run selector and it should pull all the relevant metadata for you. For example is this url https://www.ncbi.nlm.nih.gov/Traces/study/?acc=GSE65022&go=go

Answer 1

[Istvan Albert]

You can connect GEO to the SRA run info like so:

esearch -query GSE65022 -db gds | elink -target sra | efetch -format runinfo

then from that you can build the command to automate data download as such (this only gets the first 10 spots to allow easy testing):

esearch -query GSE65022 -db gds | elink -target sra | efetch -format runinfo | cut -d ',' -f 1 | grep SRR | xargs fastq-dump -X 10 --split-files

remove the limit of -X 10 when getting all the data.

[biolab]

Thank you very much, Istvan. The command you provided is really helpful!

[JC]

I wonder if search can retrieve strain information like shown in runInfo table (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRR1761531&go=go ) or SRX summary information (https://www.ncbi.nlm.nih.gov/gds/?term=SRX844624 )

[Istvan Albert]

There is an XML file that contains all the information that is displayed, though getting the data out can be somewhat convoluted. For example:

esearch -db sra -query SRR1761531 | efetch > summary.xml
cat summary.xml | xtract -Pattern SAMPLE_ATTRIBUTE -element TAG,VALUE

would produce:

source_name Leaf tissue
cultivar    Nipponbare
tissue  leaf
treatment   control
developmental stage Vegetative stage