Screen for sequencing vector using 5' cutoff of 70%, a 3' cutoff of 90% and default 5' primer position of 30. The batch of files to process are named in files.in, the names of the passed files are written to files.pass and the names of those that fail to files.fail.
vector_clip -s -L70 -R90 -m30 -pfiles.pass -f files.fail files.in
Screen for sequencing vector using 5' cutoff of 60%, a 3' cutoff of 80% and default 5' primer position of 30. The batch of files to process are named in files.in, the names of the passed files are written to files.pass and the names of those that fail to files.fail. This shows that the default search is for sequencing vector.
vector_clip -m30 -pfiles.pass -f files.fail files.in
Screen for sequencing vector using 5' cutoff of 60%, a 3' cutoff of 80% and a vector-primer-pair file called vpfile. Only the 20 bases closest to the cloning site will be used for the 5' search. The batch of files to process are named in files.in, the names of the passed files are written to files.pass and the names of those that fail to files.fail.
vector_clip -v vpfile -V20 -pfiles.pass -f files.fail files.in
Screen transposon data using 5' cutoff of 80%, a 3' cutoff of 85%, a match length of 10 and a vector-primer-pair file called vector_primer_file. The batch of files to process are named in files.in, the names of the passed files are written to files.pass and the names of those that fail to files.fail.
vector_clip -i vector_primer_file -L 80 -R 85 -l 10 -pfiles.pass \-f files.fail files.in
Screen for cloning vector using the old algorithm with a word length of 4, summing 7 diagonals and diagonal cutoff score of 0.4. The batch of files to process are named in files.in, the names of the passed files are written to files.pass and the names of those that fail to files.fail.
vector_clip -c -w4 -n7 -d0.4 -pfiles.pass -f files.fail files.in
Screen for cloning vector using the probability based algorithm with a word length of 4 and probability cutoff of 1.0e-13. The batch of files to process are named in files.in, the names of the passed files are written to files.pass and the names of those that fail to files.fail.
vector_clip -c -P 1.0e-13 -pfiles.pass -f files.fail files.in
Screen for 3' primer using a cutoff of 75%. The batch of files to process are named in files.in, the names of the passed files are written to files.pass and the names of those that fail to files.fail.
vector_clip -h -R75 -pfiles.pass -f files.fail files.in
Screen for sequencing vector rearrangements using a cutoff of 20 bases. The batch of files to process are named in files.in, the names of the passed files are written to files.pass and the names of those that fail to files.fail.
vector_clip -r -l20 -pfiles.pass -f files.fail files.in