first previous next last contents

Extract_fastq

NAME

extract_fastq -- extracts sequence and quality from a trace or experiment file.

SYNOPSIS

extract_fastq [-(abi|alf|scf|ztr|exp|pln)] [-good_only] [-clip_cosmid] [-fasta_out] [-output output_name] [input_name] ...

DESCRIPTION

extract_fastq extracts the sequence and quality information from binary trace files or Experiment files. The input can be read either from standard input or read from files listed directly as arguments or contained within a "file of filenames". Output is either sent to standard output or a named file. It contains the sequence and confidence stored in single-line fastq format.

OPTIONS

-abi, -alf, -scf, -ztr, -exp, -pln
Specify an input file format. This is not usually required as extract_seq will automatically determine the correct input file type. This option is supplied incase the automatic determination is incorrect (which is possible, but has never been observed).
-output file
The sequence will be written to file instead of standard output.
-fofn file_of_filenames
Read the reading names from file_of_filenames with one per line.

SEE ALSO

See section ExperimentFile(4).

See section scf(4).

@xref{Man-extract_seq extract_seq(1),Man-extract_seq extract_seq(1),extract_seq.1,,}. Read(4)


first previous next last contents
Last generated on 25 November 2011.