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Question: Human genome RNA Seq fastq file
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gravatar for styliae
4.4 years ago by
styliae • 0
United States
styliae • 0 wrote:

How long does it take to upload and visualize a human genome FASTq file in Galaxy? Thank you.
rna-seq • 1.5k views
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modified 4.4 years ago by Martin Čech ♦♦ 4.9k • written 4.4 years ago by styliae • 0
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gravatar for fubar
4.4 years ago by
fubar ♦ 1.1k
Australia
fubar ♦ 1.1k wrote:

Specifics matter a lot in trying to answer your question so perhaps you should measure this yourself with your own data and setup because like "how long is a piece of string", the answer varies, depending on the specifics of the string. On my local lightly loaded Galaxy instance, from upload to visualisation might take an hour for a 5GB fastq but YMMV.

Uploads are interweb dependant and Trackster takes a while to generate indexes, so it might take a few minutes to a few days depending on specifics such as how large a fastq file and whether it needs grooming; the workload on the specific Galaxy instance; the quality of the internet connection and so on.

 

 
ADD COMMENT • link written 4.4 years ago by fubar ♦ 1.1k
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