I'd think you didn't get your reversal of the tag-sequence right

I modified this to:

         print "tag \t= $tag\n";
         my $RC_tag = reverse($tag);
         print "RC_tag \t= $RC_tag\n";
         $RC_tag =~ tr/ACTGactg/TGACtgac/;
         print "RC_tag \t= $RC_tag\n";

[download]

This would print:

 tag         = ACGACACGTAT
 RC_tag      = TATGCACAGCA
 RC_tag      = ATACGTGTCGT

[download]

Which one would be correct?

In your original code,

        my $tag = $tag_obj->seq;
        print "tag = ",$tag,"\n";
        my $RC_tag = reverse $tag =~ tr/ACTGactg/TGACtgac/;

[download]

$RC_tag would be the number '11', which probably isn't what you want.

Regards

mwa

In reply to Re: Regex Match Problem by mwah
in thread Regex Match Problem by twaddlac

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