UsingAnExistingRecombinationMap
1 Introduction
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
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:
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 (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.
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 . . .
Note the last columns is the recombination rate of hermaphrodites; This can be ignored if only males and females are simulated.
