Downloading FASTQ files from ArrayExpress very slow
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20 months ago
f.morgana • 0

Hi all,

I am trying to download FASTQ files from ArrayExpress from a particular publication but it is going at an extremely slow rate. I started with attempting to download one FASTQ file of 3.85 GB. After a while I get the notification that it failed to download.

Is this a known problem? How I can efficiently download these files? There are many files to be downloaded from this publication.

Looking forward to your suggestions!

Many thanks in advance, Florencia

sequencing scRNAseq ArrayExpress FASTQ • 902 views
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You may want to get the data from NCBI. Most of data is now available via Amazon cloud links. If you can post accession numbers I can take a look.

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Thanks for your rapid responses genomax and ATpoint!

@ genomax many thanks for your suggestion, here is the concerned accession number: E-MTAB-8581. I think I managed to find the files now on NCBI but I cannot find where to download the actual FASTQ files. Do you have any idea how I could retrieve those?

Here's the link: https://www.ncbi.nlm.nih.gov/biosample/?term=E-MTAB-8581&utm_source=gquery&utm_medium=search

Or am I doing it wrong?

Cheers, Florencia

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@ genomax: Thanks so much genomax, you have been so helpful, I will give this a try!

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20 months ago
ATpoint 55k

ArrayExpress is part of ENA/EBI and there is maintenance work going on that could explain poor performance: https://www.ebi.ac.uk/about/news/service-news/ena-data-submission-service-webin-disruptions-11th-27th-march

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20 months ago
GenoMax 110k

@Florencia: Use sra-explorer tool here. Search with term PRJEB36131 (which is the project for this set). Increase the result number to 105 (there are 103 samples). Then follow the directions here to download the URL's you need for SRA (use SRA downloads tab which is the second one on results : C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks

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