Question: issue with fastQ reads download from NCBI-SRA database?
gravatar for Kumar
16 months ago by
Kumar40 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 • 432 views
ADD COMMENTlink modified 16 months ago by Researcher60 • written 16 months ago by Kumar40

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 16 months ago • written 16 months ago by Researcher60

OP was talking about downloading fastq firectly, not sra.

ADD REPLYlink written 16 months ago by ATpoint44k
gravatar for ATpoint
16 months ago by
ATpoint44k 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 16 months ago by ATpoint44k
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