Question: issue with fastQ reads download from NCBI-SRA database?
gravatar for Dineshkumar K
6 months ago by
Kasaragod, Kerala, India
Dineshkumar K30 wrote:

I am trying to download the following Bacterial genome fastq data from the NCBI-SRA database, NCBI-SRA weblink. It was sequenced by paired end manner, but when I tried to download it from the following link by pasting the SRA accession number fastQ download link, I could able to download only one file. If I am right, paired end sequence should have two fastq files such as, reverse and forward?. Therefore, please let me know, how to download both reverse and forward reads for the same. Thank you in advance.

sequencing ngs fastq sra ncbi • 229 views
ADD COMMENTlink modified 6 months ago by Researcher50 • written 6 months ago by Dineshkumar K30

I agree with ATpoint, additionally you can even get fastq file for each read by downloading SRA files which have .sra extension. You can use sra toolkits’s fastq-dump command with its --split-files option for splitting it into 2 fastq.

ADD REPLYlink modified 6 months ago • written 6 months ago by Researcher50

OP was talking about downloading fastq firectly, not sra.

ADD REPLYlink written 6 months ago by ATpoint32k
gravatar for ATpoint
6 months ago by
ATpoint32k wrote:

You can get the fastq files (which are indeed paired-end) directly from the ENA, see Select the files under FASTQ files (FTP). I do not know what this tool you link does, but ENA is a good choice. If you ever want to batch-download files from ENA, e.g. enture studies see Fast download of FASTQ files from the European Nucleotide Archive (ENA)

ADD COMMENTlink written 6 months ago by ATpoint32k
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