Dinh 2011/NOTES/2011-7-18

From ZhangLabWiki
Jump to navigation Jump to search

DMR330K Suppressor Oligos for 96 more efficient probes[edit]

  1. Script, input is tab separated file containing sorted read counts in the first column and H2 arm of probes in the second column
#!/usr/bin/perl -w
my %oligos;
while(my $line = <STDIN>){
	chop($line);
	$oligos{$line} = 1;
}
open(INFILE, "$ARGV[0]") || die("Error in opening ouput file!\n");
while(my $line = <INFILE>){
	chop($line);
	my @f = split "\t", $line;
	$f[1] =~ s/CG/YG/g;
	my $oligo = "ATCCGATC".$f[1]."TCG";
	next if($oligos{$oligo});
	print $oligo, "\n";
}
close(INFILE);
  1. File:220KSuppOligos.txt
  2. File:330KSuppOligos.txt