From a1f6d42123774730f57075913773c542cbcf45b6 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Fri, 28 Mar 2014 10:23:01 -0400 Subject: fix links and headers --- README.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 4e37d52..c351ad5 100644 --- a/README.md +++ b/README.md @@ -10,16 +10,16 @@ PI: http://brisson.bio.upenn.edu/ * [Example Usage](#example-usage) * [SGA User Interface](#sga-user-interface) * [Setting Tunable Parameters](#setting-tunable-parameters) - * [Running individual Steps](#running-individual-steps) - * [Manually scoring specific mer combinations](#manually-scoring-specific-mer-combinations-from-file) - * [Manually score all combinations from file](#manually-score-all-combinations-from-file) + * [Running Individual Steps](#running-individual-steps) + * [Manually Scoring Specific Mer Combinations From List ](#manually-scoring-specific-mer-combinations-from-list) + * [Manually Score All Combinations From List](#manually-score-all-combinations-from-list) * [Table of Tunable Parameters](#tunable-parameters) * [Equations](#equations) * [Mer Selectivity](#mer-selectivity) * [Scoring Equation](#score-function) * [Output](#output) - * [Select Mers](#select_mers.py-output) - * [Score Mers](#score_mers.py-output) + * [Select Mers](#select_merspy-output) + * [Score Mers](#score_merspy-output) ## Requirements To use this you'll need: @@ -60,7 +60,7 @@ SGA without issue. to run this all you need to do is run SelectiveGenomeAmiplifc Would you like to output your inserted variables to a string you can later paste? (Y/N/Default=y): n Run SelectiveGenomeAmplification? (Y/N/Default=y): y -### Setting Tunable Variables +### Setting Tunable Parameters SGA allows for many tunable parameters, which are all explained in the chart below. For user customizable variables, they need to be passed in as @@ -90,7 +90,7 @@ valid steps are these: This function does not try to be smart, so use it wisely. -### Manually scoring specific mer combinations from file +### Manually scoring specific mer combinations from list Users can manually score combinations of mers they choose using the score\_mers.py script. @@ -107,7 +107,8 @@ The combination file should look like this: each row is combination to be scored. -### Manually score all combinations from file +### Manually score all combinations from list + Users can manually score all combinations of mers they choose using the score\_mers.py script. -- cgit v1.2.1