FastQC analysis

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2.9 years ago

anjalivasudevan98 ▴ 40

Hii,

Could anyone please tell me if I can carry out the FastQC analysis using data available online and not in my system? The sequence data that I want to check is huge so was wondering if there was any way to access them online through FastQC?

Many thanks in advance

FastQC metagenome_data • 983 views

ADD COMMENT • link 2.9 years ago by anjalivasudevan98 ▴ 40

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Take an account in one of the public galaxy servers. Galaxy can import data from URL. Once data is imported, run fastQC on the data. Download the results. There might be restriction on data usage on public servers. Make sure that data is within the limits and once you are done, delete the downloaded data.

ADD REPLY • link 2.9 years ago by cpad0112 21k

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We need some more information to help. Where do you get your data from? What is the total size of the data to be analyzed? As quick idea assuming you are using a unix-like OS, where wget is available:

wget -O - 'url_to_your_data'  | fastqc 'arguments here'

I am not sure anymore from the top of my head if FASTQC can read from stdin, but I would guess so

ADD REPLY • link 2.9 years ago by ResearchR ▴ 120

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Thank you, both of you!

My file size is currently a little more that 2GB. But I might have to work on bigger files.

I installed FastQC in Linux platform, which in turn is installed via virtual box.

ADD REPLY • link 2.9 years ago by anjalivasudevan98 ▴ 40

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