Downloading Fastq files from ENA using FTP
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4.0 years ago

Hi all,

I would like to download all the .fq files used in the study PRJNA350777.

Link is here: http://www.ebi.ac.uk/ena/data/view/PRJNA350777

How do I go about downloading all the .fq files from this study using FTP?

Thanks for the help, Nikelle

RNA-Seq ena download fastq • 5.7k views
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The only way to get these fastq files through FTP, is to use each individual files location, since they are in different directories based on their accession number.

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4.0 years ago
GenoMax 104k

Option 1: Not FTP based. Click on "Bulk download files" button on the page you linked. Allow Java app to run. Select all files .. download.

Option 2: Click on "TEXT" button to download a listing of all the files. There are multiple columns in the file, some of which contain FTP location links. Use the links under fastq_ftp for FTP in batch. Couple of example lines below.

study_accession sample_accession    secondary_sample_accession  experiment_accession    run_accession   tax_id  scientific_name instrument_model    library_layout  fastq_ftp   fastq_galaxy    submitted_ftp   submitted_galaxy    sra_ftp sra_galaxy  cram_index_ftp  cram_index_galaxy
PRJNA350777 SAMN05945976    SRS1762137  SRX2271034  SRR4454232  9606    Homo sapiens    Illumina HiSeq 2500 PAIRED  ftp.sra.ebi.ac.uk/vol1/fastq/SRR445/002/SRR4454232/SRR4454232_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR445/002/SRR4454232/SRR4454232_2.fastq.gz   ftp.sra.ebi.ac.uk/vol1/fastq/SRR445/002/SRR4454232/SRR4454232_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR445/002/SRR4454232/SRR4454232_2.fastq.gz           ftp.sra.ebi.ac.uk/vol1/srr/SRR445/002/SRR4454232    ftp.sra.ebi.ac.uk/vol1/srr/SRR445/002/SRR4454232        
PRJNA350777 SAMN05945976    SRS1762137  SRX2271034  SRR4454233  9606    Homo sapiens    Illumina HiSeq 2500 PAIRED  ftp.sra.ebi.ac.uk/vol1/fastq/SRR445/003/SRR4454233/SRR4454233_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR445/003/SRR4454233/SRR4454233_2.fastq.gz   ftp.sra.ebi.ac.uk/vol1/fastq/SRR445/003/SRR4454233/SRR4454233_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR445/003/SRR4454233/SRR4454233_2.fastq.gz           ftp.sra.ebi.ac.uk/vol1/srr/SRR445/003/SRR4454233    ftp.sra.ebi.ac.uk/vol1/srr/SRR445/003/SRR4454233
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