CSC

Options

Usage: vector_clip [options] file_of_filenames
Where options are:
    [-s mark sequencing vector]      [-c mark cloning vector]
    [-h hgmp primer]                 [-r vector rearrangements]
    [-w word_length (4)]             [-n num_diags (7)]
    [-d diagonal score (0.35)]       [-l minimum match (20)]
    [-L minimum % 5' match (60)]     [-R minimum % 3' match (80)]
    [-m default 5' position]         [-t test only]
    [-M Max vector length (100000)]  [-P max Probability]
    [-v vector_primer filename]      [-i vector_primer filename]
    [-V vector_primer length]
    [-p passed fofn]                 [-f failed fofn]

Options:

-s

Mark sequencing vector. Searches for 5' primer, 3' running into vector.

-c

Mark cloning vector. Searches both strands for cloning vector.

-h

Hgmp primer. Searches 3' end for a primer.

-i vector_primer filename

Mark transposon data.

-r

Vector rearrangements. Searches for sequencing vector rearrangements.

-t

Test only. Does not change the experiment files, displays hits.