fastx_clipper¶

run fastx_clipper

Commands¶

output

type: map

source: input

category: output

optional: {}

pattern: ./*.fq

adaptor: ADAPTER string. default is CCTTAAGG (dummy adapter).

type: string

default: CCTTAAGG

optional: True
adaptor_and_bases: Keep the adapter and N bases after it.

type: integer

default: 0

optional: True
compress_output: Compress output with GZIP.

type: boolean

default: False

optional: True
debug_output: DEBUG output.

type: boolean

default: False

optional: True
help: help screen

type: boolean

default: False

optional: True
keep_unknown_nuc_seq: keep sequences with unknown (N) nucleotides. default is to discard such sequences.

type: boolean

default: False

optional: True
out_adaptor_only_seq: Report Adapter-Only sequences.

type: boolean

default: False

optional: True
rm_clipped_seq: Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).

type: boolean

default: False

optional: True
rm_non_clipped_seq: Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).

type: boolean

default: False

optional: True
rm_short_seq: discard sequences shorter than N nucleotides. default is 5.

type: integer

default: 5

optional: True
verbose: 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.

type: boolean

default: False

optional: True