Talk:20.109(S14):Phylogenetic and primer analyses (Day7): Difference between revisions
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Line 11: | Line 11: | ||
|F | |F | ||
|Carson Beach | |Carson Beach | ||
| | |[[Media: TR-308-alignment-FINAL.mas]] | ||
|- | |- | ||
|312 | |312 | ||
Line 23: | Line 23: | ||
|F | |F | ||
|Carson Beach | |Carson Beach | ||
| | |[[Media: WF-290-alignment-FINAL.mas]] | ||
|- | |- | ||
|274 | |274 | ||
Line 29: | Line 29: | ||
|M | |M | ||
|Carson Beach | |Carson Beach | ||
| | |[[Media: WF-274-alignment_FINAL.mas]] | ||
|- | |- | ||
|286 | |286 | ||
Line 35: | Line 35: | ||
|M | |M | ||
|Carson Beach | |Carson Beach | ||
| | |[[Media: WF-286-alignment-FINAL.mas]] | ||
|- | |- | ||
|294 | |294 | ||
Line 41: | Line 41: | ||
|M | |M | ||
|Carson Beach | |Carson Beach | ||
| | |[[Media: WF-294-Alignment-FINAL.mas]] | ||
|- | |- | ||
|304 | |304 | ||
Line 47: | Line 47: | ||
|M | |M | ||
|South Bay Center | |South Bay Center | ||
|[[Media: TR-304-Alignment- | |[[Media: TR-304-Alignment-FINAL.mas]] | ||
|- | |- | ||
|252 | |252 | ||
Line 53: | Line 53: | ||
|M | |M | ||
|South Bay Center | |South Bay Center | ||
| | |[[Media: TR-252-Alignment_finalv1.mas]] | ||
|- | |- | ||
|260 | |260 | ||
Line 59: | Line 59: | ||
|M | |M | ||
|South Bay Center | |South Bay Center | ||
| | |[[Media: WF260alignment-final2.mas]] | ||
|- | |- | ||
|} | |} | ||
Line 88: | Line 88: | ||
|308 | |308 | ||
|[[Media:TRRed308C_1.txt]] | |[[Media:TRRed308C_1.txt]] | ||
| | |Nonspecific insertion | ||
|[[Media:TRRed308C3_.txt]] | |[[Media:TRRed308C3_.txt]] | ||
| | |No significant matches found | ||
| | |Nonspecific insertion | ||
|[[Media:TRRed308_C6.txt]] | |[[Media:TRRed308_C6.txt]] | ||
| | |Poor sequencing data | ||
|[[Media:TRRed308C8.txt]] | |[[Media:TRRed308C8.txt]] | ||
|[[Media: | |[[Media:TRRed_308_final.xls]] | ||
| | |See below row | ||
| | |See below row | ||
|- | |- | ||
|Red | |Red | ||
|LT | |LT | ||
|308 | |308 | ||
| | |No priming | ||
|[[Media:TRRed308C2B.txt]] | |[[Media:TRRed308C2B.txt]] | ||
|[[Media:TRRed308C3B.txt]] | |[[Media:TRRed308C3B.txt]] | ||
|[[Media:TRRed308C4B.txt]] | |[[Media:TRRed308C4B.txt]] | ||
| | |Too short (300bp) | ||
|[[Media:TRRed308C6_B.txt]] | |[[Media:TRRed308C6_B.txt]] | ||
| | |Nonspecific insertion | ||
|[[Media:TRRed308C8B.txt]] | |[[Media:TRRed308C8B.txt]] | ||
|[[Media: | |[[Media:TRRed_308_final.xls]] | ||
| | |See below row | ||
| | |See below row | ||
|- | |- | ||
|All | |All | ||
Line 126: | Line 126: | ||
| | | | ||
|[[Media:TRRed308star.xlsx]] | |[[Media:TRRed308star.xlsx]] | ||
|[[Media:TR-308-alignment- | |[[Media:TR-308-alignment-3.mas]] | ||
|[[Media:TR-308- | |[[Media:TR-308-tree1.pdf]] | ||
|- | |- | ||
|Orange | |Orange | ||
Line 216: | Line 216: | ||
| | | | ||
|[[Media: TRGreen304CB.xlsx]] | |[[Media: TRGreen304CB.xlsx]] | ||
|[[Media: TR-304-Alignment- | |[[Media: TR-304-Alignment-FINAL.mas]] | ||
|[[Media: TR-304-Tree-Final.pdf]] | |[[Media: TR-304-Tree-Final.pdf]] | ||
|- | |- | ||
Line 227: | Line 227: | ||
|[[Media: TRGreen304C12.txt]] | |[[Media: TRGreen304C12.txt]] | ||
|[[Media: TRGreen304C13.txt]] | |[[Media: TRGreen304C13.txt]] | ||
| | | | ||
|[[Media: TRGreen304C15.txt]] | |[[Media: TRGreen304C15.txt]] | ||
| | | | ||
|[[Media: TRGreen304CR.xlsx]] | |[[Media: TRGreen304CR-FINAL.xlsx]] | ||
|[[Media: TR-304-Alignment-Final.mas]] | |[[Media: TR-304-Alignment-Final.mas]] | ||
|[[Media: TR-304-Tree-Final.pdf]] | |[[Media: TR-304-Tree-Final.pdf]] | ||
Line 245: | Line 245: | ||
| | | | ||
| | | | ||
| | |[[Media: TRBlueKT.xlsx]] | ||
|[[Media: TR-304-Alignment- | |[[Media: TR-304-Alignment-FINAL.mas]] | ||
|[[Media: TR-304-Tree-Final.pdf]] | |[[Media: TR-304-Tree-Final.pdf]] | ||
|- | |- | ||
Line 335: | Line 335: | ||
|[[Media:WFRed286_2.xlsx]] | |[[Media:WFRed286_2.xlsx]] | ||
|[[Media:WF-286-alignment-partial.mas]] | |[[Media:WF-286-alignment-partial.mas]] | ||
|[[Media:WF-286-Tree- | |[[Media:WF-286-Tree-final.pdf]] | ||
|- | |- | ||
|Red | |Red | ||
Line 389: | Line 389: | ||
|[[Media:WFYellow294(1)C3.txt]] Short sequence | |[[Media:WFYellow294(1)C3.txt]] Short sequence | ||
|Early termination | |Early termination | ||
|[[Media:WFYellow294(1)C5.txt]] | |[[Media:WFYellow294(1)C5.txt]] | ||
|Very poor quality -- can't read | |Very poor quality -- can't read | ||
|[[Media:WFYellow294(1)C7.txt]] Only used reverse sequence | |[[Media:WFYellow294(1)C7.txt]] Only used reverse sequence | ||
Line 395: | Line 395: | ||
|[[Media: WFYellow294(1).xlsx]] | |[[Media: WFYellow294(1).xlsx]] | ||
|[[Media: WF-294-Alignment.mas]] | |[[Media: WF-294-Alignment.mas]] | ||
| | |[[Media: WF-294-Tree-FINAL.pdf]] | ||
|- | |- | ||
|Yellow | |Yellow | ||
Line 420: | Line 420: | ||
| | | | ||
| | | | ||
| | |[[Media: WFGreen209C7.txt]] | ||
| | | | ||
|[[Media: WFGreen290.xlsx]] | |[[Media: WFGreen290.xlsx]] | ||
Line 431: | Line 431: | ||
| | | | ||
| | | | ||
|[[Media: WFGreen290C3B.txt]] | |||
|[[Media: WFGreen290C4B.txt]] | |||
| | | | ||
| | | | ||
| | |[[Media: WFGreen290C7B.txt]] | ||
|[[Media: WFGreen290C8B.txt]] | |||
|[[Media: WFGreen290B.xlsx]] | |||
|[[Media: | |[[Media:WF-290-alignment.mas]] | ||
|[[Media: | |[[Media:WF-290-Tree.pdf]] | ||
|[[Media:WF-290-alignment | |||
|[[Media:WF-290-Tree | |||
|- | |- | ||
|Blue | |Blue | ||
Line 505: | Line 505: | ||
|260 | |260 | ||
| | | | ||
|[[Media:WFPurple260-2C.txt]] | |||
|[[Media:WFPurple260-3C.txt]] | |||
|[[Media:WFPurple260-4C.txt]] | |||
|[[Media:WFPurple260C5B.txt]] [[Media:WFPurple260-5C.txt]] | |||
|[[Media:WFPurple260-6C.txt]] | |||
| | | | ||
|No priming | |No priming | ||
| | |[[Media:WFPurple260worksheet(updated).xlsx]] | ||
|[[Media: | |[[Media: WF260alignment-final.mas]] | ||
|[[Media: WF260Tree-final.pdf]] | |||
|[[Media: | |||
|- | |- | ||
|Purple | |Purple | ||
Line 566: | Line 566: | ||
|[[Media:WFWhite260C1.txt]] | |[[Media:WFWhite260C1.txt]] | ||
|short sequence | |short sequence | ||
| | |no priming | ||
| | |short sequence | ||
| | |no priming | ||
|[[Media:WFWhite260C6.txt]] | |[[Media:WFWhite260C6.txt]] | ||
|[[Media:WFWhite260C7.txt]] | |[[Media:WFWhite260C7.txt]] | ||
|[[Media: WFWhite260C8.txt]] | |[[Media: WFWhite260C8.txt]] | ||
|[[Media | |[[Media: WFWhite260.xlsx]] | ||
|[[Media: WF260alignment-partial.mas]] | |[[Media: WF260alignment-partial.mas]] | ||
|[[Media: WF260Tree-partial.pdf]] | |[[Media: WF260Tree-partial.pdf]] | ||
Line 582: | Line 582: | ||
| | | | ||
| | | | ||
| | |[[Media:WFWhite260C12.txt]] | ||
| | |[[Media:WFWhite260C13.txt]] | ||
|[[Media:WFWhite260C14.txt]] | |[[Media:WFWhite260C14.txt]] | ||
| | | | ||
| | | | ||
|[[Media:WFwhite260.xlsx]] | |[[Media:WFwhite260.xlsx]] | ||
| | |[[Media:WF260alignment-final2.mas]] | ||
| | |[[Media:WF260TreeFinal2.pdf]] | ||
|- | |- | ||
|} | |} | ||
Line 620: | Line 620: | ||
| Red | | Red | ||
| Green | | Green | ||
|[[Media:TR3.BMP]] | |||
|- | |- | ||
| T/R 4 | | T/R 4 | ||
Line 625: | Line 626: | ||
| Pink | | Pink | ||
| Blue | | Blue | ||
|[[Media:TR4.BMP]] | |||
|- | |- | ||
|} | |} | ||
Line 657: | Line 659: | ||
| Red | | Red | ||
| Orange | | Orange | ||
| | |[[Media:WF3.BMP]] | ||
|- | |- | ||
| W/F 4 | | W/F 4 | ||
Line 663: | Line 665: | ||
| Yellow | | Yellow | ||
| Pink | | Pink | ||
| | |[[Media:WF4.BMP]] | ||
|- | |- | ||
|} | |} |
Latest revision as of 11:22, 9 March 2014
General notes and updates
Sample # | Species | Sex | Location | Final MEGA File |
308 | RBG | F | Carson Beach | Media: TR-308-alignment-FINAL.mas |
312 | RBG | F | Carson Beach | Media: TR-312-alignment_FINAL.mas |
290 | RBG | F | Carson Beach | Media: WF-290-alignment-FINAL.mas |
274 | RBG | M | Carson Beach | Media: WF-274-alignment_FINAL.mas |
286 | RBG | M | Carson Beach | Media: WF-286-alignment-FINAL.mas |
294 | RBG | M | Carson Beach | Media: WF-294-Alignment-FINAL.mas |
304 | HG | M | South Bay Center | Media: TR-304-Alignment-FINAL.mas |
252 | HG | M | South Bay Center | Media: TR-252-Alignment_finalv1.mas |
260 | HG | M | South Bay Center | Media: WF260alignment-final2.mas |
T/R microbiota
Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].
W/F microbiota
Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].
T/R microsporidia gels
Gel number | Reference samples | Group 1 | Group 2 | Picture |
---|---|---|---|---|
T/R 1 | Specificity (VC, EH, mixture) | Orange | Yellow | Media:TR1.BMP |
T/R 2 | Specificity (VC, EH, mixture) | Blue | W/F Green | Media:TR2.BMP |
T/R 3 | Sensitivity (EH: lo, mid, hi) | Red | Green | Media:TR3.BMP |
T/R 4 | Sensitivity (EH: lo, mid, hi) | Pink | Blue | Media:TR4.BMP |
W/F microsporidia gels
Gel number | Reference samples | Group 1 | Group 2 | Picture |
---|---|---|---|---|
W/F 1 | Specificity (VC, EH, mixture) | Blue | Purple | Media:WF1.BMP |
W/F 2 | Specificity (VC, EH, mixture) | Silver | White | Media:WF2.BMP |
W/F 3 | Sensitivity (EH: lo, mid, hi) | Red | Orange | Media:WF3.BMP |
W/F 4 | Sensitivity (EH: lo, mid, hi) | Yellow | Pink | Media:WF4.BMP |