Page Comparison

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.

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