NAME

fastx_clipper - FASTA/Q Clipper

DESCRIPTION

usage: fastx_clipper [-h] [-a ADAPTER] [-D] [-l N] [-n] [-d N] [-c] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com)

[-h]

= This helpful help screen.

[-a ADAPTER] = ADAPTER string. default is CCTTAAGG (dummy adapter). [-l N] = discard sequences shorter than N nucleotides. default is 5. [-d N] = Keep the adapter and N bases after it.

(using '-d 0' is the same as not using '-d' at all. which is the default).

[-c]

= Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).

[-C]

= Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).

[-k]

= Report Adapter-Only sequences.

[-n]

= keep sequences with unknown (N) nucleotides. default is to discard such sequences.

[-v]

= Verbose - report number of sequences.

If [-o] is specified,

report will be printed to STDOUT.

If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.

[-z]

= Compress output with GZIP.

[-D]

= DEBUG output.

[-M N]

= require minimum adapter alignment length of N.

If less than N nucleotides aligned with the adapter - don't clip it.

[-i INFILE] = FASTA/Q input file. default is STDIN.

[-o OUTFILE] = FASTA/Q output file. default is STDOUT.

SEE ALSO

The quality of this automatically generated manpage might be insufficient. It is suggested to visit

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

to get a better layout as well as an overview about connected FASTX tools.