clip -- an Experiment File sequence clipper
-s start_offset] [
-M maximum_extent] [
-u r_unknown_1] [
-W r_length_2] [
-l l_length_1] [
-L l_length_2] [
-Y l_unknown_2] file ...
Clip is a simple program to decide how much of the 3' end of a
sequence, stored as an Experiment File, should be clipped off and ignored
during assembly. The decision is made by simply counting the numbers of
unknown bases (eg
N) found within windows slid left to
right along the sequence.
The file arguments, of which there can be several, are processed one at a
time. Each argument is assumed to be a valid Experiment File. The sequence
is read from the Experiment File
SQ identifier; clipping is performed;
QR identifiers are appended to the file.
The right clip position is calculated by sliding to the right a window of
r_length_1 along the sequence starting from base
start_offset. We stop once we find greater than or equal to
r_unknown_1 unknown bases. At this stage two choices are available; to
place our clip at the start position of our first window or to proceed from
our current position plus half of
r_length_1 using a second window. In
the latter case we perform a similar operation to the first window, except
r_unknown_2 parameters. We will then
set the clip to be the start position of this second window.
The left clip position is calculated by sliding a window to the left starting
start_offset. The algorithm used is identical to the right
clip position except that the
l_len_2 parameters are used.
To only use one window (the default parameters) set the
parameter to be 0 using
The default arguments are
-s 70 -m 0 -M 999999 -w 100 -u 5 -W 0 -U 0 -l 20 -y 3 -L 0 -Y 0."
QLclip value of less than extent bases into the sequence then use extent as the
QRclip value of more than extent bases into the sequence then use extent as the
To clip a batch of sequences listed in the `fofn' file with a minimum left clip value of 20 bases use:
clip -m 20 `cat fofn`
See section ExperimentFile(4).See section trace_clip.