SLIDE 32 Vector screening Vector screening
Example Example: :
cross cross_match _match seqfile seqfile.fasta .fasta vector vector. .seq seq – –minmatch minmatch 10 10 – –minscore minscore 20 20 – –screen screen > > screen screen.out .out where where: :
‘seqfile seqfile.fasta’ is a file .fasta’ is a file containing multiple reads containing multiple reads in FASTA in FASTA format format
‘vector vector. .seq’ seq’ is a file is a file containing the vector sequences containing the vector sequences
‘-
minmatch’ and ‘ ‘-
minscore’ are are parameters parameters for for pairwise alignment pairwise alignment
‘-
screen’ creates a file a file named seqfile named seqfile.fasta. .fasta.screen containing vector screen containing vector-
masked versions versions of
the original
sequences. . Any region Any region matching any part matching any part of a
vector sequence sequence is is replaced by Xs replaced by Xs. .
‘screen screen.out’ .out’ contains contains a a list list of
the matches found
the .‘ .‘screen’ screen’ file is file is the the input for input for phrap phrap
if a ‘.qual’ file was created was created (i.e. (i.e. seqfile seqfile.fasta.qual) .fasta.qual) , it , it has has to to be renamed be renamed to to ( (seqfile seqfile.fasta. .fasta.screen screen.qual) .qual) – – phredPhrap phredPhrap script script automatically performs automatically performs this this step step! !
AG AG-
FMVZ-
USP
