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FASTAQ-SEARCH_FOR_SEQ(1) User Commands FASTAQ-SEARCH_FOR_SEQ(1)

NAME

fastaq_search_for_seq - Find all exact matches to a string (and its reverse complement)

DESCRIPTION

usage: fastaq_search_for_seq [options] <infile> <outfile> <search_string>

Searches for an exact match on a given string and its reverse complement, in every sequence of input sequence file. Case insensitive. Guaranteed to find all hits

positional arguments:

infile
Name of input file
outfile
Name of outputfile. Tab-delimited output: sequence name, position, strand
search_string
String to search for in the sequences

optional arguments:

-h, --help
show this help message and exit
April 2020 fastaq 3.17.0