Efficient way to download all .bam files in a project from ENA to remote server
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2.3 years ago
4galaxy77 2.7k

I'd like to batch download all the .bam files in a particular ENA project to my cluster. It seems like there are some nice tools, like SRA explorer, and this post here [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA), which are great for batch downloading the fastq files. Is there an equivalent for downloading .bam files as well?

It's possible to just click "Download all", but this will work if you are trying to download to your local machine, but won't work downloading to a remote server.

ENA bam • 833 views
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Hi, I guess the links from the tutorial only need minimal modifications for bam files. Can you share a link to a file, I will then see how the links look and suggest some code. By the way, does ENA store BAMs, I thought they use CRAM exclusively?


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