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  • ln -s <path> says to create a symbolic link link (symlink) to the specified file (or directory) in the current directory
    • always use the -s option to avoid creating a hard link, which behaves quite differently
  • the default link name corresponds to the last name component in <path>
    • you can name the link file differently by supplying an optional link_file_name.
  • it is best to change into (cd) the directory where you want the link before executing ln -s
  • a symbolic link can be deleted without affecting the linked-to file
  • the -f (force) option says to overwrite any existing symbolic link with the same name

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  • find returns a list of matching file paths on its standard output
  • ln wants its files listed as arguments, not on standard input
    • so the paths are piped to the standard input of xargs
  • xargs takes the data on its standard input and calls the specified function (here ln -sf -t .) with that data as the function's argument list.

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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:

...                           Compressed input and output is supported and
auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
standard input/output. ...

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

And the usage also 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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titleAnswer...

The cutadapt usage doesn't say anything directly about diagnostics:

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

But again, reading in the Output: options section:

   -o FILE, --output=FILE
        Write trimmed reads to FILE. FASTQ or FASTA format is
        chosen depending on input. The summary report is sent
        to standard output. Use '{name}' in FILE to
        demultiplex reads into multiple files. Default: write
        to standard output

Careful reading of this suggests that:

  • When the -o option is omitted, and output goes to standard output,
    • diagnostics must be written to standard error
      • so can be redirected to a log file with 2> trim.log
    • cutadapt -a CGTAATTCGCG small.fq 1> trimmed.fastq 2> trim.log
  • But when the trimmed output is sent to a file with the -o output.fastq option,
    • diagnostics are written to standard output
      • so can be redirected to a log file with 1> trim.log
    • cutadapt -a CGTAATTCGCG -o trimmed.fastq  small.fq 1> trim.log

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