This is the command fastx_clipper that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
fastx_clipper - FASTA/Q Clipper
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 ([email protected])
[-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
[-C] = Discard clipped sequences (i.e. - keep only sequences which did not contained the
[-k] = Report Adapter-Only sequences.
[-n] = keep sequences with unknown (N) nucleotides. default is to discard such
[-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
[-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.
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