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| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-28 10:23:01 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-28 10:23:01 -0400 |
| commit | a1f6d42123774730f57075913773c542cbcf45b6 (patch) | |
| tree | a7eb29f390e46c0f1b14972544f7b06983e2b826 /README.md | |
| parent | 5f536cd247316f17adab74e369b3a2de48c7838d (diff) | |
fix links and headers
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 17 |
1 files changed, 9 insertions, 8 deletions
@@ -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. |