From 5f536cd247316f17adab74e369b3a2de48c7838d Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Fri, 28 Mar 2014 10:18:21 -0400 Subject: Add headers, move stuff, toc --- README.md | 51 ++++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 40 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 92abded..4e37d52 100644 --- a/README.md +++ b/README.md @@ -3,12 +3,28 @@ SelectiveGenomeAmplification PI: http://brisson.bio.upenn.edu/ - - +## Table of Contents + +* [Requirements](#requirements) +* [Setup](#setup) +* [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) +* [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) + ## Requirements To use this you'll need: - - A Uenix environment + - A Unix environment - kmer_total_count, a kmer counter available here: http://github.com/mutantturkey/dna-utils/ - bash or compliant shell. @@ -20,7 +36,7 @@ To use this you'll need: make sudo make install -## Usage Examples +## Example Usage Standard use of (SGA) SelectiveGenomeAmplification is easy. it takes two arguments, the foreground and background @@ -28,6 +44,24 @@ the foreground and background SelectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta; less PfalciparumGenome_HumanGenome/final_mers +### SGA User Interface +SGA also comes with a easy to use user prompt called SelectiveGenomeAmplificationUI. +It allows for a less experienced user to use +SGA without issue. to run this all you need to do is run SelectiveGenomeAmiplifcationUI and you'll see a series of prompts asking the user about tunables like below + + Where would you like to temporary files to be stored? (Default=$output_directory/.tmp): + Where would you like to count files to be stored? (Default=$output_directory/.tmp): + maximum mer size you would like to pick? (Default=12): 10 + minimum mer size you would like to pick? (Default=6): 7 + eliminate mers that appear less frequently on average than this number ? (Default=50000): 25000 + ..... + Input the path to your foreground file:target.fa + Input the path to your background file:humangenome.fa + 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 + 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 environmental variables like so: @@ -35,9 +69,6 @@ environmental variables like so: max_mer_distance=5000 max_select=6 min_mer_range=6 max_mer_range=12 \ SelectiveGenomeAmplification.sh PfalciparumGenome.fasta half.fasta -SGA also comes with a easy to use user prompt called SelectiveGenomeAmplificationUI. -It allows for a less experienced user to use -SGA without issue. ### Running individual steps @@ -95,9 +126,7 @@ The mer file should look like this: each row is a separate mer. do not put multiple mers on one line. -## Customizable variables - -range of mers, min and max +## Tunable Parameters variable | default | notes :---- | :---- | ---- | :---- @@ -125,7 +154,7 @@ primer\_weight | 0 | How much extra weight to give to sets with a higher number Here's what we are using to determine our scoring and selectivity -### Selectivity +### Mer Selectivity Our selectivity is what we use to determine what top $max\_check mers are checked later on in our scoring function. Currently we use this formula: -- cgit v1.2.3