CSC

Extract Sequence

Description

This module uses the extract_seq program to extract the sequence information from binary trace files, Experiment files, or from the old Staden format plain files. The output contains the sequences split onto lines of at most 60 characters each, in plain or fasta format. The input files are passed unchanged onto subsequent modules.

Option: Output only the good sequence

When reading an experiment file or trace file containing clip marks, output only the good sequence which is contained within the boundaries marked by the QL, QR, SL, SR, CL, CR and CS line types.

Option: Consider cosmid as good sequence

When the Output only the good sequence option is specified this controls whether the cosmid sequence should be considered good.

Option: Output in fasta format

Specifies that the output should be in fasta format rather than plain text.

Option: Output in one file only

If this option is selected then the output from every sequence is sent to one file. This is best used with the Output in fasta format option selected, and is useful for feeding into BLAST searches, for example. The file to write to is specified in the File name filed. If this option is unselected then the output is sent to separate files, one per sequence. The output files have the same name as the input files, except with an extra suffix specified in the File name suffix field.