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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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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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