Post date: May 26, 2016 11:1:34 PM
Test run with family 143, need to repeat this will combined families. All of the files are in /uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/melissa_mappingfams/lm2map/. I also need to figure out how to best deal with the sex chromosome. But, this all appears to work fairly well.
1. Prepare data file
perl ../scripts/makeLinkageFormat.pl sub_offspringGenotypes_filtered2x_fam143.txt
2. Filter data
java -cp ~/source/lepmap2/bin/ Filtering data=lm_fam143.txt epsilon=0.01 dataTolerance=0.01 missingLimit=10 keepAlleles=1 > data_fam143.txt
***
Mendel error statistics:
0->0 : 0
0->1 : 0
0->2 : 0
Error rate = 0.0
1->0 : 0
1->1 : 0
1->2 : 0
Error rate = 0.0
2->0 : 0
2->1 : 0
2->2 : 0
Error rate = 0.0
0,2->0,2 : 228736
0,2->1 : 0
1,2->1,2 : 0
1,2->0 : 0
Error rate = 0.0
***
Filtering markers based on segregation distortion
Removed 771 markers from family 143
Maternally informative markers = 5282 (of 12090)
Paternally informative markers = 6451
Maternally or paternally informative markers = 11319
***
Removed 1544 markers
3. Female LGs
java -cp ~/source/lepmap2/bin/ SeparateChromosomes data=data_fam143.txt lodLimit=5 femalePrior=0.05 informativeMask=2 sizeLimit=5 > flgs_fam143.txt
***
Mendel error statistics:
0->0 : 0
0->1 : 0
0->2 : 0
Error rate = 0.0
1->0 : 0
1->1 : 0
1->2 : 0
Error rate = 0.0
2->0 : 0
2->1 : 0
2->2 : 0
Error rate = 0.0
0,2->0,2 : 212086
0,2->1 : 0
1,2->1,2 : 0
1,2->0 : 0
Error rate = 0.0
***
Filtering markers based on segregation distortion
Removed 0 markers from family 143
Maternally informative markers = 4885 (of 12090)
Paternally informative markers = 6033
Maternally or paternally informative markers = 10546
***
LOD(25, 0) = 6.977937445473155
LOD(24, 0) = 6.685684111175531
LOD(24, 1) = 5.287878197260586
LOD(23, 2) = 3.7755199624146547
LOD(25, 0) = 6.977937445473155
LOD(24, 0) = 6.685684111175531
LOD(24, 1) = 5.287878197260586
LOD(23, 2) = 3.7755199624146547
Family 143
Number of different markers = 2007
Using LOD score 5.0
Computing pair-wise LOD scores 1.2.3.4.5.6.7.8.9.10 all done
number of LGs = 27 singles = 10283
Removing LG 24 (as too small) with size 4
Removing LG 25 (as too small) with size 2
Removing LG 26 (as too small) with size 2
Removing LG 27 (as too small) with size 2
Number of LGs = 23, markers in LGs = 3840, singles = 8250
5. Add singles to map
java -cp ~/source/lepmap2/bin/ JoinSingles flgs_fam143.txt data=data_fam143.txt lodLimit=4 lodDifference=1 > flgs_js_fam143.txt
Number of joined markers in chr 1 is 38
Number of joined markers in chr 2 is 34
Number of joined markers in chr 3 is 24
Number of joined markers in chr 4 is 26
Number of joined markers in chr 5 is 25
Number of joined markers in chr 6 is 27
Number of joined markers in chr 7 is 23
Number of joined markers in chr 8 is 29
Number of joined markers in chr 9 is 37
Number of joined markers in chr 10 is 42
Number of joined markers in chr 11 is 37
Number of joined markers in chr 12 is 21
Number of joined markers in chr 13 is 22
Number of joined markers in chr 14 is 25
Number of joined markers in chr 15 is 13
Number of joined markers in chr 16 is 31
Number of joined markers in chr 17 is 17
Number of joined markers in chr 18 is 19
Number of joined markers in chr 19 is 19
Number of joined markers in chr 20 is 10
Number of joined markers in chr 21 is 10
Number of joined markers in chr 22 is 3
Number of joined markers in chr 23 is 4
joined 536 single markers, non-conflicting LOD score > 4.350864189212862
Number of LGs = 23, markers in LGs = 4403, singles = 7687
6. perl script to assign (or remove assignments) LGs at the scaffold-level
perl addMalesFilter.pl fscaflg_fam143.txt
assigned LGs for 747 scaffolds, failed to assign LGs for 6389 scaffolds
this corresponds to about 35.5% of SNPs with LG assignments, and does not include sex chromosome assignments
7. Order markers, use male and female recombination
java -cp ~/source/lepmap2/bin/ OrderMarkers map=slgs_js_fam143.txt data=data_fam143.txt minError=0.01 initRecombination=0.05 0.000000001 learnRecombinationParameters=1 0 > order