Question: Fastq-dump paired downloader does not retrieve the SRA files from the accession number, how tio fix?
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gravatar for dublukkvas1954
4.2 years ago by
dublukkvas19540 wrote:

Fastq-dump paired downloader does not retrieve the SRA files from the accession number, how tio fix? This module works on Galaxy cloud instance.

galaxy fastq-dump • 1.4k views
ADD COMMENTlink modified 4.2 years ago by Shicheng Guo8.5k • written 4.2 years ago by dublukkvas19540

Galaxy related questions are best posted over at Galaxy Biostars.

You can grab the fastq files from EBI-ENA if you don't want to wait for a resolution to your original question and upload them to Galaxy.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by GenoMax94k

I know, thx, are there alternative Galaxy modules to get SRA files automatically from the accession number and did you face a similar trouble with fastq-dump downloader?

ADD REPLYlink written 4.2 years ago by dublukkvas19540

Try the NCBI SRA toolkit:

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

ADD REPLYlink written 4.2 years ago by Tonor430
0
gravatar for Shicheng Guo
4.2 years ago by
Shicheng Guo8.5k
Shicheng Guo8.5k wrote:

Several different bugs have been found for fastq-dump. However, what you should do is make sure the fastq-dump should be most latest version. You need to update the software frequently since old version can not works well after new version come out. It is ridiculous but it is truth. if it still don't work after you use latest version, then give up and use wget or curl to download the fastq or SRA from ftp server. for example:

for i in SRR1648425 SRR1648426 SRR1648427 SRR1648428
do
       wget http://sra-download.ncbi.nlm.nih.gov/srapub/$i
       mv $i $i.sra
       fastq-dump --gzip --split-files $i.sra
done
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Shicheng Guo8.5k
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