Collect and format Coregonus genetic map input data for MapComp analysis
MapComp https://github.com/enormandeau/mapcomp
bwa (using 0.7.12-r1039)
samtools (using v.1.9)
The following species have been analyzed previously. Check this repo for more info: https://github.com/bensutherland/2016_ms_sfonmap
- Coho Salmon (Kodama et al. 2014)
- Chinook Salmon (Brieuc et al. 2014)
- Rainbow Trout (Palti et al. 2015)
- Chum Salmon (Waples et al. 2016)
- Sockeye Salmon (Larson et al. 2015)
- Brook Charr (Sutherland et al. 2016)
- Atlantic Salmon (Lien et al. 2011)
- Lake Whitefish (Gagnaire et al. 2013)
- Northern Pike (Rondeau et al. 2014)
In the present analysis, we will analyze the following Coregonus species:
- Lake Whitefish (Coregonus clupeaformis) (see above)
- European Whitefish (Coregonus lavaretus albock) (de Kayne et al. 2018)
- Cisco (Coregonus artedi) (Blumstein et al. in prep)
...in addition to the following species (one per genus):
- Northern Pike (see above)
- Atlantic Salmon (see above)
- Brook Charr (see above)
- Chinook Salmon (see above)
...to obtain the new European Whitefish and Cisco maps, and to obtain the reduced species from previous analyses, follow the steps below
Download raw data for all species in the previous analysis from:
https://www.dropbox.com/s/s5gbp1sak54cwdd/markers.csv?dl=0
Put the downloaded file into 02_input_materials, and run within R:
01_scripts/salmonid_maps_v1_subset.r
...this will produce a combined input file for the species of interest from the previous analysis, entitled 02_input_materials/data_v1_subset.csv
Follow the instructions in 00_resources/data_sources.md
...this will collect European Whitefish and Cisco and put into the file 02_input_materials/markers_2.csv
Clone mapcomp onto your computer, in the same level directory as coregonus_mapcomp:
cd ..
git clone https://github.com/enormandeau/mapcomp.git
cd ./mapcomp
The rest of the instructions should be followed from within the mapcomp directory.
# Get data
cp ./../coregonus_mapcomp/02_input_materials/markers_2.csv ./02_data/
cp ./../coregonus_mapcomp/02_input_materials/data_v1_subset.csv ./02_data/
# Combine and remove header
cat 02_data/data_v1_subset.csv 02_data/markers_2.csv | grep -vE 'mname' - > 02_data/markers.csv
# Prepare input fasta
./01_scripts/00_prepare_input_fasta_file_from_csv.sh 02_data/markers.csv
See how many markers and how many species:
grep '>' 02_data/markers.fasta | awk -F"_" '{ print $1 }' - | sort | uniq -c | less
| Markers | Species |
|---|---|
| 20450 | >Cart |
| 17067 | >Cartfnodup |
| 6340 | >Cartm |
| 3438 | >Cclu |
| 5395 | >Clav |
| 524 | >Eluc |
| 6352 | >Otsh |
| 3826 | >Sfon |
| 5917 | >Ssal |
Change the variable GENOME_FILE in ./mapcomp and the 01_scripts/01_bwa_align_reads.sh
# Run the analysis
./mapcomp
# Output figures are available in 04_figures
Bring in the original mapcomp excel table:
/Users/wayne/Documents/general_projects/04_continuing_salmonid_MapComp/corr_bw_LGs_Sfonv3.4_wRT_2016-12-28.xlsx