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scp usage is similar to cp in that it copies from a <source> to a <destination>, but uses remote machine addressing to qualify either the <source> or the <destination> but not both.

Remote machine addressing looks like this: <user_account>@<hostname>:<source_or_destination>

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titleAnswer...

The cutadapt usage says an input.fastq file is a required argument:

    cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq

But again, reading a bit further we see:


Input may also be in FASTA format. Compressed input and output is supported and
auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
standard input/output. Without the -o option, output is sent to standard output.



This suggests input can be specified in 2 ways:

  • from a file, using the -o option
    • cutadapt -a CGTAATTCGCG -o trimmed.fastq  small.fq
  • from standard input if the input.fastq argument is replaced with a dash ( - )
    • cat small.fq | cutadapt -a CGTAATTCGCG -o trimmed.fastq  -

And also says that the input.fastq file can be provided in one of three compression formats.

Where does cutadapt write its diagnostic output by default? How can that be changed?

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