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.
-L
minimum percentage match 5' end (60)
-
sequencing vector searches and transposon search
-R
minimum percentage match 3' end (80)
-
sequencing vector searches and transposon search
-m
minimum 5' position
-
allows a minimum 5' end cutoff to be set if a sufficiently good match is not
found (i.e. it is really a default 5' cutoff position).
If a value of -1 is used the program will set the cutoff to be the
distance between the primer and the cloning site.
-v
vector-primer-pair filename
-
sequencing vector search using vector-primer-pair file
-V
vector_primer length
-
the length of the sequence stored in the vector_primer file to use for
the 5' search
-w
word_length (4)
-
cloning vector search hash length
-P
probability
-
cloning vector search, (a score less likely than P is a match)
-n
num_diags (7)
-
cloning vector search, old score based algorithm: number of diagonals to combine
-d
diagonal score (0.35)
-
cloning vector search, old score based algorithm
-l
minimum match (20)
-
sequencing vector rearrangements and transposon search minimum match length
-M
maximum vector length (100000)
-
all algorithms, reset for vectors >100000 bases
-p
passed fofn
-
file of file names for passed files
-f
failed fofn
-
file of file names for failed files
- input fofn ...
-
input file of file names
Last generated on 25 November 2011.