issue with fastQ reads download from NCBI-SRA database?

Question

[Kumar]

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.

[Researcher]

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.

[ATpoint]

OP was talking about downloading fastq firectly, not sra.

Answer 1

[ATpoint]

You can get the fastq files (which are indeed paired-end) directly from the ENA, see https://www.ebi.ac.uk/ena/data/view/SRR1631220. 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)