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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 pair filename]
    [-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.
-r
Vector rearrangements. Searches for sequencing vector rearrangements.
-t
Test only. Does not change the experiment files, displays hits.

Parameters (defaults in brackets)

-L minimum percentage match 5' end (60)
sequencing vector searches
-R minimum percentage match 3' end (80)
sequencing vector searches
-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
-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 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

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/vector_clip_4.html