Recent changes to UsingAnExistingRecombinationMap

UsingAnExistingRecombinationMap modified by Christos Vlachos

Christos Vlachos — Wed, 27 Jun 2018 10:17:12 -0000

--- v5
+++ v6
@@ -2,7 +2,7 @@

 #1 Introduction

-In this part of the manual we will show how   the recombination map of *Drosophila melanogaster* can be downloaded and tranformed into files that can be used directly for simulations with MimicrEE2.
+In this part of the manual we will show how   the recombination map of *Drosophila melanogaster* can be downloaded and transformed into files that can be used directly for simulations with MimicrEE2.

 #2 Requirements
 [Recombination map for *Drosophila melanogaster*](https://petrov.stanford.edu/cgi-bin/recombination-rates_updateR5.pl)

UsingAnExistingRecombinationMap modified by Robert Kofler

Robert Kofler — Mon, 25 Jun 2018 14:26:35 -0000

--- v4
+++ v5
@@ -1,13 +1,13 @@
 [TOC]

-# Introduction
+#1 Introduction

 In this part of the manual we will show how   the recombination map of *Drosophila melanogaster* can be downloaded and tranformed into files that can be used directly for simulations with MimicrEE2.

-#Requirements
+#2 Requirements
 [Recombination map for *Drosophila melanogaster*](https://petrov.stanford.edu/cgi-bin/recombination-rates_updateR5.pl)

-##Convert recombination map to MimicrEE2 format
+#3 Convert recombination map to MimicrEE2 format
 In order to download the recombination map of* Drosophila melanogaster* please follow the link above and use the option batch query to submit for which genomic windows, estimates should be returned. In our example we use windows of 100 kb. Your input in the query should look like this:

 ~~~~
@@ -46,7 +46,7 @@

 The output can be easily copy-pasted to a new file (e.g.: **dmel_rr.txt**).  Ignore the first line (column titles) and copy the information for genomic windows only.  What we  keep in order to obtain recombination files compatible with MimicrEE2 is the first column (genomic locus) and the sixth column (Comeron midpoint recombination rate. 

-### Simple recombination map
+## Simple recombination map

 Assuming that the recombination rate is identical in all sexes we can use the following unix command to convert the recombination rate into a format compatible with MimicrEE2.

@@ -72,7 +72,7 @@
 .
 ~~~~

-### Sex specific recombination rate
+## Sex specific recombination rate
 In this example we will use different recombination rates for male, female and hermaphrodite individuals. We assume that males have no recombination.
 For more details on the input files please have a look [here](https://sourceforge.net/p/mimicree2/wiki/InputData/).

UsingAnExistingRecombinationMap modified by Robert Kofler

Robert Kofler — Thu, 21 Jun 2018 11:59:40 -0000

--- v3
+++ v4
@@ -5,7 +5,7 @@
 In this part of the manual we will show how   the recombination map of *Drosophila melanogaster* can be downloaded and tranformed into files that can be used directly for simulations with MimicrEE2.

 #Requirements
-[Recombination map for *Drosophila Melanogaster*](https://petrov.stanford.edu/cgi-bin/recombination-rates_updateR5.pl)
+[Recombination map for *Drosophila melanogaster*](https://petrov.stanford.edu/cgi-bin/recombination-rates_updateR5.pl)

 ##Convert recombination map to MimicrEE2 format
 In order to download the recombination map of* Drosophila melanogaster* please follow the link above and use the option batch query to submit for which genomic windows, estimates should be returned. In our example we use windows of 100 kb. Your input in the query should look like this:

UsingAnExistingRecombinationMap modified by Robert Kofler

Robert Kofler — Thu, 21 Jun 2018 11:34:49 -0000

--- v2
+++ v3
@@ -101,3 +101,4 @@
 .
 ~~~~

+**Note** the last columns is the recombination rate of hermaphrodites; This can be ignored if only males and females are simulated.

UsingAnExistingRecombinationMap modified by Robert Kofler

Robert Kofler — Thu, 21 Jun 2018 11:33:53 -0000

--- v1
+++ v2
@@ -2,13 +2,13 @@

 # Introduction

-In this part of the manual we will present how  data from genomic resources, such as the recombination map of *Drosophila Melanogaster* can be downloaded and tranformed into files that can be used directly for simulations with MimicrEE2.
+In this part of the manual we will show how   the recombination map of *Drosophila melanogaster* can be downloaded and tranformed into files that can be used directly for simulations with MimicrEE2.

 #Requirements
 [Recombination map for *Drosophila Melanogaster*](https://petrov.stanford.edu/cgi-bin/recombination-rates_updateR5.pl)

 ##Convert recombination map to MimicrEE2 format
-In order to download the recombination map of* Drosophila Melanogaster *please follow the link above and use the option batch query to submit for which genomic windows, estimates should be returned. In our example we use windows of 100 kb. Your input in the query should look like this:
+In order to download the recombination map of* Drosophila melanogaster* please follow the link above and use the option batch query to submit for which genomic windows, estimates should be returned. In our example we use windows of 100 kb. Your input in the query should look like this:

 ~~~~
 2L:0..100000
@@ -44,7 +44,37 @@

 ~~~~

-The output can be easily copy-pasted to a new file (let's name it **dmel_rr.txt**).  Ignore the first line (column titles) and copy the information for genomic windows only.  What we need to keep in order to have our MimicrEE2 recombination file is the first column that indicates the genomic locus and the midpoint comeron recombination rate. In our example we will use different recombination rates for male, female and hermaphrodite individuals (male flies have no recombination). For more details on the input files please have a look [here](https://sourceforge.net/p/mimicree2/wiki/InputData/).  In our hypothetical population we will have 50% males and 50% females and subsequently the recombination rate of hermaphrodites will be equal to 0.  
+The output can be easily copy-pasted to a new file (e.g.: **dmel_rr.txt**).  Ignore the first line (column titles) and copy the information for genomic windows only.  What we  keep in order to obtain recombination files compatible with MimicrEE2 is the first column (genomic locus) and the sixth column (Comeron midpoint recombination rate. 
+
+### Simple recombination map
+
+Assuming that the recombination rate is identical in all sexes we can use the following unix command to convert the recombination rate into a format compatible with MimicrEE2.
+
+~~~~
+awk '{printf("%s\t%s\n", $1,$6)}' dmel_rr.txt | sed '1 s/.*/[cM\/Mb]/g' > mimicree2_recombination_map
+~~~~
+
+Your converted file should now look like this:
+~~~~
+[cM/Mb]
+2L:100000..200000  0.00
+2L:200000..300000  0.00
+2L:300000..400000  0.23
+2L:400000..500000  0.23
+2L:500000..600000  1.99
+2L:600000..700000  1.41
+2L:700000..800000  1.06
+2L:800000..900000  2.35
+2L:900000..1000000 3.05
+2L:1000000..1100000    3.40
+.
+.
+.
+~~~~
+
+### Sex specific recombination rate
+In this example we will use different recombination rates for male, female and hermaphrodite individuals. We assume that males have no recombination.
+For more details on the input files please have a look [here](https://sourceforge.net/p/mimicree2/wiki/InputData/). 

 The file above can be easily transformed into MimicrEE2 format using the bash one-liner shown below:
 ~~~~
@@ -71,26 +101,3 @@
 .
 ~~~~

-A file like this is ready to be sed as input for simulations with MimicrEE2.  Of course it is possible to ignore sex and simulate only hermaphrodites. This case is even simpler and the following bash one-liner can be used:
-
-~~~~
-awk '{printf("%s\t%s\n", $1,$6)}' dmel_rr.txt | sed '1 s/.*/[cM\/Mb]/g' > mimicree2_recombination_map
-~~~~
-
-Your converted file should now look like this:
-~~~~
-[cM/Mb]
-2L:100000..200000  0.00
-2L:200000..300000  0.00
-2L:300000..400000  0.23
-2L:400000..500000  0.23
-2L:500000..600000  1.99
-2L:600000..700000  1.41
-2L:700000..800000  1.06
-2L:800000..900000  2.35
-2L:900000..1000000 3.05
-2L:1000000..1100000    3.40
-.
-.
-.
-~~~~

UsingAnExistingRecombinationMap modified by Christos Vlachos

Christos Vlachos — Tue, 12 Jun 2018 11:35:44 -0000

Introduction
Requirements
- Convert recombination map to MimicrEE2 format

Introduction

In this part of the manual we will present how data from genomic resources, such as the recombination map of Drosophila Melanogaster can be downloaded and tranformed into files that can be used directly for simulations with MimicrEE2.

Requirements

Recombination map for Drosophila Melanogaster

Convert recombination map to MimicrEE2 format

In order to download the recombination map of Drosophila Melanogaster please follow the link above and use the option batch query to submit for which genomic windows, estimates should be returned. In our example we use windows of 100 kb. Your input in the query should look like this:

2L:0..100000
2L:100000..200000
2L:200000..300000
2L:300000..400000
2L:400000..500000
2L:500000..600000
2L:600000..700000
2L:700000..800000
2L:800000..900000
2L:900000..1000000
2L:1000000..1100000
.
.
.

After your request you will be prompted to the output page that should look like this:

Genomic locus       RRC Startpoint rate         RRC Midpoint rate       RRC Endpoint rate       Comeron Startpoint rate         Comeron Midpoint rate       Comeron Endpoint rate      
2L:0..100000        0.00        0.00        0.00        0.00        0.00        0.00      
2L:100000..200000       0.00        0.00        0.00        0.00        0.00        0.00      
2L:200000..300000       0.00        0.00        0.00        0.00        0.00        0.00      
2L:300000..400000       0.00        0.00        0.00        0.00        0.23        0.23      
2L:400000..500000       0.00        0.00        0.00        0.23        0.23        0.23      
2L:500000..600000       0.00        2.80        2.82        0.23        1.99        1.99      
2L:600000..700000       2.82        2.84        2.86        1.99        1.41        1.41      
2L:700000..800000       2.86        2.88        2.90        1.41        1.06        1.06      
2L:800000..900000       2.90        2.91        2.93        1.06        2.35        2.35      
2L:900000..1000000          2.93        2.95        2.97        2.35        3.05        3.05      
2L:1000000..1100000         2.97        2.98        3.00        3.05        3.40        3.40

The output can be easily copy-pasted to a new file (let's name it dmel_rr.txt). Ignore the first line (column titles) and copy the information for genomic windows only. What we need to keep in order to have our MimicrEE2 recombination file is the first column that indicates the genomic locus and the midpoint comeron recombination rate. In our example we will use different recombination rates for male, female and hermaphrodite individuals (male flies have no recombination). For more details on the input files please have a look here. In our hypothetical population we will have 50% males and 50% females and subsequently the recombination rate of hermaphrodites will be equal to 0.

The file above can be easily transformed into MimicrEE2 format using the bash one-liner shown below:

awk '{printf("%s\t%s\t%s\t%s\n", $1,0,$6,0)}' dmel_rr.txt | sed '1 s/.*/[cM\/Mb]/g' > mimicree2_recombination_map

Your converted file should now look like this:

[cM/Mb]
2L:0..100000    0   0.00    0
2L:100000..200000   0   0.00    0
2L:200000..300000   0   0.00    0
2L:300000..400000   0   0.23    0
2L:400000..500000   0   0.23    0
2L:500000..600000   0   1.99    0
2L:600000..700000   0   1.41    0
2L:700000..800000   0   1.06    0
2L:800000..900000   0   2.35    0
2L:900000..1000000  0   3.05    0
2L:1000000..1100000 0   3.40    0
.
.
.

A file like this is ready to be sed as input for simulations with MimicrEE2. Of course it is possible to ignore sex and simulate only hermaphrodites. This case is even simpler and the following bash one-liner can be used:

awk '{printf("%s\t%s\n", $1,$6)}' dmel_rr.txt | sed '1 s/.*/[cM\/Mb]/g' > mimicree2_recombination_map

Your converted file should now look like this:

[cM/Mb]
2L:100000..200000   0.00
2L:200000..300000   0.00
2L:300000..400000   0.23
2L:400000..500000   0.23
2L:500000..600000   1.99
2L:600000..700000   1.41
2L:700000..800000   1.06
2L:800000..900000   2.35
2L:900000..1000000  3.05
2L:1000000..1100000 3.40
.
.
.