run fastx_clipper
output
type: mapsource: inputcategory: outputoptional: {}pattern: ./*.fq
ADAPTER string. default is CCTTAAGG (dummy adapter).
Keep the adapter and N bases after it.
Compress output with GZIP.
DEBUG output.
help screen
keep sequences with unknown (N) nucleotides. default is to discard such sequences.
Report Adapter-Only sequences.
Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).
Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).
discard sequences shorter than N nucleotides. default is 5.
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.