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cutadapt -o versus >

Hi, I am following a protocol for CLIP data analysis, and their cutadapt options are using both -o and > it is paired end data, so under -o they put R1.out -p R2.out, but then they add > R_output.metrics

I tried looking it up in cutadapt manual, and it looked to me as if -o and > are mutually exclusive... anyone knows what the > means here?

thanks!

cutadapt
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updated by Devon Ryan Devon Ryan • written by blur blur

1 answer

> means "redirect the standard output to a file" on Linux and Macs. This is independent from any particular program.

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written by Devon Ryan Devon Ryan

so, this is just where the cutadapt report will end up? thanks!

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written by blur blur

Yes, R_output.metrics will contain the report which is printed to standard error. Just try and see...

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written by dariober dariober

you are absolutly right - thank you!

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written by blur blur

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