reformatted parentage data

RAnalysis/Data/Popgen/Parentages/F1_parentage.csv

@@ -1,27 +1,27 @@
-Sample.ID,key
-adapter_trim.F0-B1,Pa
-adapter_trim.F0-B10,Mo
-adapter_trim.F0-B11,Pa
-adapter_trim.F0-B12,NA
-adapter_trim.F0-B13,Mo
-adapter_trim.F0-B14,Mo
-adapter_trim.F0-B15,Fa
-adapter_trim.F0-B16,Mo
-adapter_trim.F0-B17,Fa
-adapter_trim.F0-B18,Fa
-adapter_trim.F0-B19,NA
-adapter_trim.F0-B2,Pa
-adapter_trim.F0-B20,Mo
-adapter_trim.F0-B21,Fa
-adapter_trim.F0-B22,Fa
-adapter_trim.F0-B23,NA
-adapter_trim.F0-B24,Fa
-adapter_trim.F0-B25,Fa
-adapter_trim.F0-B26,Mo
-adapter_trim.F0-B27,Mo
-adapter_trim.F0-B3,Pa
-adapter_trim.F0-B4,Pa
-adapter_trim.F0-B5,Fa
-adapter_trim.F0-B6,Fa
-adapter_trim.F0-B7,Pa
-adapter_trim.F0-B9,Fa
+Broodstock_ID,Seqdata_ID_raw,Seqdata_ID,Batch_1,Batch_2,Batch_3,Batch_4,Batch_5,key,Ped
+1,adapter_trim.F0-B1,F0-B1,F,F,M,M,M,Pa,Both
+2,adapter_trim.F0-B2,F0-B2,F,M,F,M,M,Pa,Both
+3,adapter_trim.F0-B3,F0-B3,NA,M,F,NA,F,Pa,Both
+4,adapter_trim.F0-B4,F0-B4,F,NA,M,M,M,Pa,Both
+5,adapter_trim.F0-B5,F0-B5,M,NA,NA,M,M,Fa,Sire
+6,adapter_trim.F0-B6,F0-B6,M,NA,M,NA,NA,Fa,Sire
+7,adapter_trim.F0-B7,F0-B7,F,M,M,F,F,Pa,Both
+9,adapter_trim.F0-B9,F0-B9,NA,M,M,M,M,Fa,Sire
+10,adapter_trim.F0-B10,F0-B10,NA,F,F,NA,F,Mo,Dam
+11,adapter_trim.F0-B11,F0-B11,M,M,M,F,F,Pa,Both
+12,adapter_trim.F0-B12,F0-B12,NA,NA,NA,NA,NA,NA,NA
+13,adapter_trim.F0-B13,F0-B13,F,F,NA,F,NA,Mo,Dam
+14,adapter_trim.F0-B14,F0-B14,NA,F,F,F,F,Mo,Dam
+15,adapter_trim.F0-B15,F0-B15,NA,NA,NA,M,M,Fa,Sire
+16,adapter_trim.F0-B16,F0-B16,NA,F,F,F,F,Mo,Dam
+17,adapter_trim.F0-B17,F0-B17,M,NA,M,NA,NA,Fa,Sire
+18,adapter_trim.F0-B18,F0-B18,NA,NA,NA,M,M,Fa,Sire
+19,adapter_trim.F0-B19,F0-B19,NA,NA,NA,NA,NA,NA,NA
+20,adapter_trim.F0-B20,F0-B20,NA,F,NA,F,NA,Mo,Dam
+21,adapter_trim.F0-B21,F0-B21,NA,NA,NA,M,M,Fa,Sire
+22,adapter_trim.F0-B22,F0-B22,NA,NA,NA,M,M,Fa,Sire
+23,adapter_trim.F0-B23,F0-B23,NA,NA,NA,NA,NA,NA,NA
+24,adapter_trim.F0-B24,F0-B24,NA,NA,M,M,M,Fa,Sire
+25,adapter_trim.F0-B25,F0-B25,M,NA,M,M,M,Fa,Sire
+26,adapter_trim.F0-B26,F0-B26,NA,F,NA,F,F,Mo,Dam
+27,adapter_trim.F0-B27,F0-B27,NA,NA,F,NA,NA,Mo,Dam

RAnalysis/Data/Popgen/Parentages/F2_parentage.csv

@@ -0,0 +1,37 @@
+Broodstock_ID,Treatment,Seqdata_ID,Batch_1,Batch_2,Batch_3,Batch_4,key,Ped
+1,Moderate,F1-B1-pH75,M,NA,NA,M,Fa,Sire
+2,Moderate,F1-B2-pH75,M,NA,NA,NA,Fa,Sire
+4,Moderate,F1-B4-pH75,NA,M,NA,M,Fa,Sire
+5,Moderate,F1-B5-pH75,NA,M,NA,M,Fa,Sire
+6,Moderate,F1-B6-pH75,F,NA,NA,F,Mo,Dam
+8,Moderate,F1-B8-pH75,NA,NA,M,NA,Fa,Sire
+9,Moderate,F1-B9-pH75,NA,M,NA,NA,Fa,Sire
+10,Moderate,F1-B10-pH75,NA,F,NA,F,Mo,Dam
+11,Moderate,F1-B11-pH75,NA,F,NA,F,Mo,Dam
+12,Moderate,F1-B12-pH75,NA,F,NA,NA,Mo,Dam
+14,Moderate,F1-B14-pH75,M,NA,NA,M,Fa,Sire
+16,Moderate,F1-B16-pH75,NA,NA,F,NA,Mo,Dam
+17,Moderate,F1-B17-pH75,F,NA,NA,NA,Mo,Dam
+18,Moderate,F1-B18-pH75,NA,NA,F,NA,Mo,Dam
+19,Moderate,F1-B19-pH75,NA,NA,F,NA,Mo,Dam
+20,Moderate,F1-B20-pH75,NA,NA,M,NA,Fa,Sire
+21,Moderate,F1-B21-pH75,F,NA,NA,NA,Mo,Dam
+24,Moderate,F1-B24-pH75,NA,NA,M,NA,Fa,Sire
+1,Low,F1-B1-pH8,NA,M,NA,M,Fa,Sire
+2,Low,F1-B2-pH8,M,NA,NA,NA,Fa,Sire
+3,Low,F1-B3-pH8,NA,NA,M,NA,Fa,Sire
+4,Low,F1-B4-pH8,M,NA,NA,NA,Fa,Sire
+5,Low,F1-B5-pH8,NA,NA,M,NA,Fa,Sire
+7,Low,F1-B7-pH8,NA,NA,M,M,Fa,Sire
+8,Low,F1-B8-pH8,F,M,NA,NA,Pa,Both
+9,Low,F1-B9-pH8,M,NA,NA,M,Fa,Sire
+10,Low,F1-B10-pH8,NA,M,NA,NA,Fa,Sire
+11,Low,F1-B11-pH8,NA,NA,NA,M,Fa,Sire
+15,Low,F1-B15-pH8,F,NA,NA,F,Mo,Dam
+17,Low,F1-B17-pH8,F,NA,NA,NA,Mo,Dam
+19,Low,F1-B19-pH8,NA,F,NA,NA,Mo,Dam
+20,Low,F1-B20-pH8,NA,F,NA,NA,Mo,Dam
+21,Low,F1-B21-pH8,NA,F,NA,F,Mo,Dam
+22,Low,F1-B22-pH8,NA,NA,F,NA,Mo,Dam
+23,Low,F1-B23-pH8,NA,NA,F,F,Mo,Dam
+25,Low,F1-B25-pH8,NA,NA,F,NA,Mo,Dam

RAnalysis/Data/Popgen/Parentages/F3_parentage.csv

@@ -0,0 +1,46 @@
+Broodstock_ID,Treatment,Seqdata_ID,Batch_1,Batch_2,Batch_3,Batch_4,key,Ped
+1,High,F3-B1-pH7,F,M,NA,NA,Pa,Both
+2,High,F3-B2-pH7,F,M,NA,NA,Pa,Both
+3,High,F3-B3-pH7,M,NA,NA,NA,Fa,Sire
+4,High,F3-B4-pH7,M,F,NA,NA,Pa,Both
+5,High,F3-B5-pH7,NA,NA,M,NA,Fa,Sire
+6,High,F3-B6-pH7,NA,F,NA,NA,Mo,Dam
+7,High,F3-B7-pH7,NA,NA,F,NA,Mo,Dam
+8,High,F3-B8-pH7,NA,NA,NA,M,Fa,Sire
+9,High,F3-B9-pH7,NA,F,NA,NA,Mo,Dam
+10,High,F3-B10-pH7,F,NA,M,NA,Pa,Both
+12,High,F3-B12-pH7,NA,NA,F,NA,Mo,Dam
+15,High,F3-B15-pH7,NA,NA,NA,F,Mo,Dam
+16,High,F3-B16-pH7,NA,NA,NA,F,Mo,Dam
+18,High,F3-B18-pH7,NA,NA,F,NA,Mo,Dam
+19,High,F3-B19-pH7,NA,NA,NA,F,Mo,Dam
+25,High,F3-B25-pH7,NA,NA,NA,M,Fa,Sire
+1,Moderate,F3-B1-pH75,NA,F,M,NA,Pa,Both
+2,Moderate,F3-B2-pH75,F,NA,NA,NA,Mo,Dam
+3,Moderate,F3-B3-pH75,NA,NA,NA,F,Mo,Dam
+5,Moderate,F3-B5-pH75,NA,F,NA,NA,Mo,Dam
+6,Moderate,F3-B6-pH75,NA,NA,F,NA,Mo,Dam
+10,Moderate,F3-B10-pH75,NA,NA,M,NA,Fa,Sire
+11,Moderate,F3-B11-pH75,F,M,NA,NA,Pa,Both
+14,Moderate,F3-B14-pH75,M,F,NA,NA,Pa,Both
+16,Moderate,F3-B16-pH75,M,NA,NA,NA,Fa,Sire
+17,Moderate,F3-B17-pH75,NA,M,F,NA,Pa,Both
+19,Moderate,F3-B19-pH75,F,NA,NA,M,Pa,Both
+21,Moderate,F3-B21-pH75,NA,NA,F,NA,Mo,Dam
+22,Moderate,F3-B22-pH75,NA,NA,NA,M,Fa,Sire
+24,Moderate,F3-B24-pH75,NA,NA,NA,F,Mo,Dam
+25,Moderate,F3-B25-pH75,NA,NA,NA,F,Mo,Dam
+1,Low,F3-B1-pH8,F,NA,NA,NA,Mo,Dam
+2,Low,F3-B2-pH8,F,NA,NA,M,Pa,Both
+3,Low,F3-B3-pH8,NA,NA,NA,M,Pa,Both
+5,Low,F3-B5-pH8,F,NA,NA,NA,Mo,Dam
+6,Low,F3-B6-pH8,NA,M,NA,F,Pa,Both
+7,Low,F3-B7-pH8,NA,M,F,NA,Pa,Both
+8,Low,F3-B8-pH8,NA,NA,M,F,Pa,Both
+10,Low,F3-B10-pH8,NA,F,NA,NA,Mo,Dam
+11,Low,F3-B11-pH8,M,NA,NA,NA,Fa,Sire
+12,Low,F3-B12-pH8,M,NA,F,NA,Pa,Both
+13,Low,F3-B13-pH8,NA,NA,F,NA,Mo,Dam
+15,Low,F3-B15-pH8,NA,F,NA,NA,Mo,Dam
+16,Low,F3-B16-pH8,NA,NA,M,F,Pa,Both
+23,Low,F3-B23-pH8,NA,F,NA,NA,Mo,Dam

RAnalysis/Data/Popgen/Parentages/README.md

@@ -0,0 +1,24 @@
+Subfolder: RAnalysis\Data\Popgen\**Parentages**
+
+**About**
+
+* *excel_workbooks*
+
+    - downloaded directly from the goolge drive for the bay scallop project
+
+    - contexts as F1, F2, and F2 Parentages
+
+    - what do we mean by *parentage* in these document titles? Contents contain the broodstock adult scallop ids
+    sorted by fertilization batches and whether sperm (male) or egg (female) gametes were used for that batch. *Parentage*
+    refers the  parents for the offspring  generation in the title. n other words,  F1 and F3 Parentages are the parent broodstock
+    F0 and F2 scallops whose gametes were fertilized to produce F1 and F3 offspring.
+
+    - **Note**: in no case were both serm and egg used for the same fertilization batch, this was critical to avoid self fertilization!
+
+
+
+* *formatted*
+
+  - the raw excel sheets were reformatted for ease of access to all data needed to reun parentage anlysis (i.e. using sequoia in R)
+
+  - files F1_Parentage, F2_Parentage, F3_Parentage