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how I can download both of the two files from ebi

Hello,

I want to download the files: SRR8611991_4_R1_001.fastq and SRR8611991_4_R2_001.fastq from https://www.ebi.ac.uk/ena/data/view/SRR8611991.

But I only can download one SRR8611991.fastq file.

How can I download both of them from ebi?

Thanks in advance for any great help!

Best,

Yue

Please see attached file.

!Screenshot-from-2020-04-07-20-58-45

rna-seq
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updated by GenoMax GenoMax • written by yueli7 yueli7

1 answer

This is again 10x data. There are independent R1,R2,I1 files in Data access tab at NCBI SRA, but unfortunately you will need to pay to download those from Google cloud or Amazon AWS. They appear to have made these three files as a single download for the link that remains free. Here is one sample. Looks like there are a total of four samples in this set.

Edit: I prefetched the single file. fastq-dump --split-files -F SRR8611994 generated three files R1,R2,I3 (they were named SRR8611994_1.fastq, SRR8611994_2.fastq, SRR8611994_3.fastq and will need to be renamed afterwards).

Note : My guess is the single file on EBI-ENA is also one that contains all three files.

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written by GenoMax GenoMax

Hello, genomax,

Thank you so much for your answer.

The only one file in EBI is the fastq file which contains 98bp (aligned to the genome). It does not have UMI+barcode and sample index files.

Thank you again!

Best,

Yue

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written by yueli7 yueli7

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