Is there a way to download all runs for SRA id like this https://www.ncbi.nlm.nih.gov/sra/?term=SRX724870 ? I manually searching the SRA on NCBI site and using fastq-dump for each one the runs. For example, I am running following three as fastq-dump -I --split-files SRX724870 gives errors.
fastq-dump -I --split-files SRR1602552
fastq-dump -I --split-files SRR1602553
fastq-dump -I --split-files SRR1602554
I have a list of SRA ids for which I am manually searching and running fastq-dump. It would be great of I can download all runs just using SRA id (e.g. SRX724870).
•
written
by
BDK_compbio
I remember that automatic expansion of container accessions is not currently available in sratoolkit.
Why don't you try this short bash script?
It automatically retrieves all SRA accessions from SRX identifier and downloads corresponding runs.
#!/bin/bash
srx_id=SRX724870
sra_ids=$(wget -qO- "http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=${srx_id}" | grep ${srx_id} | cut -f1 -d",")
for sra_id in "${sra_ids[@]}"; do
fastq-dump "${sra_id}"
done
It gives the following error
2021-06-10T05:07:51 fastq-dump.2.9.1 err: item not found while constructing within virtual database module - the path 'SRR1602552 SRR1602553 SRR1602554' cannot be opened as database or table
I think that the error has occurred because you wrote your code at the line 8 like this:
fastq-dump "${sra_ids}"
It would have produced a command line below
$ fastq-dump "SRR1602552 SRR1602553 SRR1602554"
So you should fix the code using the variable ${sra_id} instead of using ${sra_ids}.
fastq-dump "${sra_id}"
or it is also okay.
fastq-dump ${sra_id}
It will produces a bunch of command lines as follows:
$ fastq-dump SRR1602552
$ fastq-dump SRR1602553
$ fastq-dump SRR1602554
I hope you solve the problem.
Also this script using e-utilities should work:
if ! type "efetch" > /dev/null; then
print "Please install E-utilitie."
fi
GSM=$1
! type "foo" > /dev/null 2>&1;
echo $GSM retrieves from NCBI GEO.....
all_data=`esearch -db sra -query $GSM |efetch -format docsum |xtract -pattern DocumentSummary -element Run@acc`
for SRR in ${all_data}
do
echo "processing" $SRR
fastq-dump -A $SRR
done
I am afraid that I may not be doing things correctly. I just copied the script into script1.sh and run sh script1.sh and it gives the following error
script1.sh: line 1: type: efetch: not found
script1.sh: line 2: print: command not found
retrieves from NCBI GEO.....
script1.sh: line 7: esearch: command not found
script1.sh: line 7: efetch: command not found
script1.sh: line 7: xtract: command not found
Log in to answer this question.
Just enter the query at sra-explorer : find SRA and FastQ download URLs in a couple of clicks and get download links for fastq files right away.