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Downloading Fastq files from ENA using FTP

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

fastq rna-seq ena
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updated by Ram Ram • written by nikelle.petrillo nikelle.petrillo

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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written by st.ph.n st.ph.n

1 answer

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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written by GenoMax GenoMax

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