From f6fe059e37d8e8ee0cb6f7acf72c8918473ad3f7 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Wed, 26 Mar 2014 14:16:34 -0400 Subject: add primer_weight to our score function --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'README.md') diff --git a/README.md b/README.md index a745b19..18334c9 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,8 @@ ignore\_mers | Not Enabled | mers to explicitly ignore, space seperated ex. igno foreground | Not Enabled | path of foreground file background | Not Enabled | path of background file max\_consecutive\_binding | 4 | The maxium number of consecutive binding nucleotides in homodimer and heterodimers -fg\_weight | 0 | How much extra weight to give higher frequency mers in fg. see "equations" +fg\_weight | 0 | How much extra weight to give higher frequency mers in fg. see "equations" (between 0 and 1) +primer\_weight | 0 | How much extra weight to give to sets with a higher number of priemrs. (between 0 and 1) ## Equations @@ -66,3 +67,6 @@ environmental variable if you wish to do so. hit = abundance of primer X (ex. 'ATGTA') in background (foreground hit / background hit) * (foreground hit ^ fg_weight) + + +### Score function -- cgit v1.2.3