From f04cf54479e739c23218f45eb22cef694f88428f Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Fri, 28 Mar 2014 09:55:16 -0400 Subject: Spelling fixes in documentation whoop wehhoop --- README.md | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 665e8b7..92abded 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ PI: http://brisson.bio.upenn.edu/ ## Requirements To use this you'll need: - - A unix environment + - A Uenix environment - kmer_total_count, a kmer counter available here: http://github.com/mutantturkey/dna-utils/ - bash or compliant shell. @@ -36,7 +36,7 @@ environmental variables like so: SelectiveGenomeAmplification.sh PfalciparumGenome.fasta half.fasta SGA also comes with a easy to use user prompt called SelectiveGenomeAmplificationUI. -It allows for a less expereienced user to use +It allows for a less experienced user to use SGA without issue. ### Running individual steps @@ -71,7 +71,7 @@ The combination file should look like this: ACGATATAT TACATAGA TATATATAT ACGTACCAT ATATTA AAATTATCAGT ATACATA ATATACAT ATATACATA ACATA - ATATACATA ATCATGATA CCAGATACATAT + ATATACATA ATCATGATA CCAGATACATAT each row is combination to be scored. @@ -86,13 +86,13 @@ score\_mers.py script. The mer file should look like this: ATATAT - TACATA - TACATAGCA - TATAGAATAC - CGTAGATA - TAGAAT + TACATA + TACATAGCA + TATAGAATAC + CGTAGATA + TAGAAT -each row is a seperate mer. do not put multiple mers on one line. +each row is a separate mer. do not put multiple mers on one line. ## Customizable variables @@ -110,28 +110,28 @@ counts\_directory | $output\_directory/.tmp | directory for counts directory tmp\_directory | $output\_directory/.tmp | temporary files directory max\_melting\_temp | 30° | maximum melting temp of mers min\_melting\_temp | 0° | minimum melting temp of mers -min\_foreground\_binding\_average | 50000 | elminate mers that appear less frequently than the average (length of foreground / # of occurances) +min\_foreground\_binding\_average | 50000 | eliminate mers that appear less frequently than the average (length of foreground / # of occurrances) max\_select | 15 | maximum number of mers to pick max\_check | 35 | maximum number of mers to select (check the top #) -ignore\_mers | Not Enabled | mers to explicitly ignore, space seperated ex. ignore\_mers="ACAGTA ACCATAA ATATATAT" -ignore\_all\_mers\_from\_files | Not Enabled | ignore any mers found in these files. space seperated. +ignore\_mers | Not Enabled | mers to explicitly ignore, space separated ex. ignore\_mers="ACAGTA ACCATAA ATATATAT" +ignore\_all\_mers\_from\_files | Not Enabled | ignore any mers found in these files. space separated. 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 +max\_consecutive\_binding | 4 | The maximum 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" (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) +primer\_weight | 0 | How much extra weight to give to sets with a higher number of primers. (between 0 and 1) ## Equations Here's what we are using to determine our scoring and selectivity -### Selecivity +### 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: By default our fg\_weight is zero. This gives no extra weight to more -frequently occuring mers, but can be set higher with the fg\_weight +frequently occurring mers, but can be set higher with the fg\_weight environmental variable if you wish to do so. hit = abundance of primer X (ex. 'ATGTA') in background @@ -143,7 +143,7 @@ environmental variable if you wish to do so. The scoring function is this: - fg_pts = all the points of each mer in the combination, and sequence ends4 + fg_pts = all the points of each mer in the combination, and sequence ends fg_mean_dist = mean distance between each point in fg_pts fg_stddev = standard deviation of distance between each point in fg_pts @@ -183,6 +183,6 @@ background count, and the mer selectivity value. (higher is better) ### score\_mers.py output -score medrs outputs a tab delmited file with 6 columns: +score mers outputs a tab delimited file with 6 columns: nb_primers Combination Score FG_mean_dist FG_stdev_dist BG_ratio -- cgit v1.2.3 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(-) (limited to 'README.md') 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 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 v1.2.3 From 7f1a5af24a5105392d0d644e4559ea85f6b8b618 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Fri, 28 Mar 2014 10:29:15 -0400 Subject: Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'README.md') diff --git a/README.md b/README.md index c351ad5..1e8e425 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ To use this you'll need: - A Unix environment - kmer_total_count, a kmer counter available here: http://github.com/mutantturkey/dna-utils/ - bash or compliant shell. - + - python 2.7.x ## Setup -- cgit v1.2.3 From af94a1600676fbc581322236c478e92f06ce3243 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Fri, 28 Mar 2014 10:30:01 -0400 Subject: Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'README.md') diff --git a/README.md b/README.md index 1e8e425..7d6680b 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ PI: http://brisson.bio.upenn.edu/ To use this you'll need: - A Unix environment - - kmer_total_count, a kmer counter available here: http://github.com/mutantturkey/dna-utils/ + - [dna-utils](http://github.com/mutantturkey/dna-utils/) - bash or compliant shell. - python 2.7.x -- cgit v1.2.3