[ fxtools trim
]
Summary
This tool can be used to select and trim sequences that contain a specified adapter sequence.
This can almost be thought of as a combination of grep
and sed
, where everything before the grep
match is
removed.
By default the adapter sequence is kept (the adapter will be a common prefix for all kept reads) but it can also be trimmed away.
Usage
# trim away sequences prefixing the adapter
fxtools trim -i <your_seq.fq.gz> -a ACTTGGA
# trim away sequences prefixing the adapter + the adapter
fxtools trim -i <your_seq.fq.gz> -a ACTTGGA --trim-adapter