Talk:20.109(S14):Phylogenetic and primer analyses (Day7): Difference between revisions

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Revision as of 19:51, 8 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]].

Team Color Team Member Gull ID Sequence 1 (txt) Sequence 2 (txt) Sequence 3 (txt) Sequence 4 (txt) Sequence 5 (txt) Sequence 6 (txt) Sequence 7 (txt) Sequence 8 (txt) Species overview (xlsx) Alignment (mas) Tree (pdf)
Red AK 308 Media:TRRed308C_1.txt Nonspecific insertion Media:TRRed308C3_.txt No significant matches found Nonspecific insertion Media:TRRed308_C6.txt Poor sequencing data Media:TRRed308C8.txt Media:TRRed_308_final.xls See below row See below row
Red LT 308 No priming Media:TRRed308C2B.txt Media:TRRed308C3B.txt Media:TRRed308C4B.txt Too short (300bp) Media:TRRed308C6_B.txt Nonspecific insertion Media:TRRed308C8B.txt Media:TRRed_308_final.xls See below row See below row
All SKH 308 Media:TR308S2.txt Media:TR308S3.txt Media:TR308S4.txt Media:TRRed308star.xlsx Media:TR-308-alignment-3.mas Media:TR-308-tree1.pdf
Orange CT-Q 312 Media:TROrange312C1_FINAL.txt‎ Media:TROrange312C2_FINAL.txt Media:TROrg312C3FINAL-FINAL.txt Media:TROrange312_FINAL-FINAL.xlsx
Orange AN 308 Media: TROrange308AC2.txt Media: TROrange308AC3.txt Media: TROrange308AC4_1.txt Media: TROrange308AC5.txt Media: TROrange308AC_1.xlsx
Yellow REDO 312 Media: 312-2final.txt Media: 312-4_FINAL.txt Media: 312-5_FINAL_fixed.txt Media: 312-7_FINAL.txt Media: 312-10_FINAL_fixed.txt Media: 312-REDO-samples_FINAL.xlsx
Yellow SW 312 Media: TRYellow312C2Final.txt Media: TRYellow312C2bFinal.txt Media: TRYellow312C6bFinal.txt Media: TRYellow312FINAL.xlsx
Yellow EL 312 Media: TRYellow3121b_FINAL.txt Media: TRYellow312C3_FINAL.txt Media: TRYellow312C3b_FINAL.txt Media: TR-312-alignment_FINAL.mas Media: TR_312_tree_FINAL.pdf
Green CB 304 Media: TRGreen304C1.txt TRGreen304C7 Reverse Media: TRGreen304CB.xlsx Media: TR-304-Alignment-Final.mas Media: TR-304-Tree-Final.pdf
Green CR 304 Media: TRGreen304C11.txt Media: TRGreen304C12.txt Media: TRGreen304C13.txt Media: TRGreen304C15.txt Media: TRGreen304CR-Final.xlsx Media: TR-304-Alignment-Final.mas Media: TR-304-Tree-Final.pdf
Blue KT 304 Media: TRBlue304C3.txt Media: TRBlueKT.xlsx Media: TR-304-Alignment-Final.mas Media: TR-304-Tree-Final.pdf
Blue MG 252 (see Pink) Media: _TR252Excel.xlsx‎ Media: TR-252-Alignment_finalv1.mas Media: TR-252-Tree-finalv1.pdf
Pink RCB 252 Media: TRPink252C1.txt Media: TRPink252C3.txt Media: TRPink252C5.txt Media: _TR252Excel.xlsx Media: TR252-only.mas Media: TR-252-Tree-finalv1.pdf
Pink HMH / MG 252 Media: TRPink252C3B_v1.txt Media: TRPink252C4B_v1.txt Media: TRPink252C5B.txt Media: TRPink252C6B.txt Media: _TR252Excel.xlsx‎ Media: TR-252-Alignment_finalv1.mas Media: TR-252-Tree-finalv1.pdf



W/F microbiota

Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].

Team Color Team Member Gull ID Sequence 1 (txt) Sequence 2 (txt) Sequence 3 (txt) Sequence 4 (txt) Sequence 5 (txt) Sequence 6 (txt) Sequence 7 (txt) Sequence 8 (txt) Species overview (xlsx) Alignment (mas) Tree (pdf)
Red TVK 286 Media:WFRed286C1.txt Media:WFRed286C2.txt Media:WFRed286C4.txt Media:WFRed286C5.txt Media:WFRed286C6.txt Media:WFRed286C7.txt Media:WFRed286_2.xlsx Media:WF-286-alignment-partial.mas Media:WF-286-Tree-partial.pdf
Red JQX 286 Media:WFRed286C1B.txt Media:WFRed286C2B.txt Media:WFRed286C3B.txt Media:WFRed286C4B.txt Media:WFRed286C5B.txt Media:WFRed286C6B.txt Media:WFRed286C8B.txt Media:WFRed286.xlsx
Orange EAK 286 Media:WFOrange286C9.txt Media:Orange286.xlsx
Orange
Yellow TCD 294(1) Media: WFYellow294(1)C1.txt Media: WFYellow294(1)C2.txt Media:WFYellow294(1)C3.txt‎ Short sequence Early termination Media:WFYellow294(1)C5.txt‎ Very poor quality -- can't read Media:WFYellow294(1)C7.txt Only used reverse sequence Media:WFYellow294(1)C8.txt Only used reverse sequence Media: WFYellow294(1).xlsx Media: WF-294-Alignment.mas Media: WF-294-Tree-FINAL.pdf
Yellow HRS 294(2) Media: WFYellow294(2)C1.txt Media: WFYellow294(2)C2.txt Media: WFYellow294(2)C3.txt Media: WFYellow294(2)C4.txt Only use sequence from Reverse Primer Media: WFYellow294(2)C5.txt Media: WFYellow294(2)C6.txt Media: WFYellow294(2)C7.txt Media: WFYellow294(2)C8.txt Does not start with AGA Media: WFYellow294(2).xlsx
Green P^2 290 Media: WFGreen209C6.txt Media: WFGreen209C7.txt Media: WFGreen290.xlsx
Green IK 290 Media: WFGreen290C3B.txt Media: WFGreen290C4B.txt Media: WFGreen290C7B.txt Media: WFGreen290C8B.txt Media: WFGreen290B.xlsx Media:WF-290-alignment.mas Media:WF-290-Tree.pdf
Blue VAM 290 Media:WFBlue290C1.txt Media:WFBlue290C2.txt Media:WFBlue290C4.txt Media:WFBlue290C8.txt Media:WFBlue290.xlsx
Blue VT 274 Very short product Media:WFBlue274C2.txt (Beginning and end of sequence is correct, middle of sequence is ambiguous due to early termination) Media:WFBlue274C3.txt No liquid culture growth Media:WFBlue274C5.txt Media:WFBlue274C6.txt No priming No priming Media:WFBlue274.xlsx Media:WF-274-alignment.mas Media:WF-274-tree.pdf
Pink MZ/GG 274 Media:WFPink274G1.ape.txt Media:WFPink274G2.ape.txt short sequence Media:WFPink274G4.ape.txt no priming Media:WFPink274G6.ape.txt poor quality Media:WFPink274G8.ape.txt Media:WFPinkSpecies.xlsx refer to blue team VT for alignment refer to blue team VT for tree
Pink GG/MZ 274 Media:WFPink274M1_shortRead.ape.txt no priming Media:WFPink274M3_shortRead.ape.txt no priming Media:WFPink274M5 short read.ape.txt Media:WFPink274M6 short read.ape.txt no priming Media:WFPink274M8.ape.txt short read no sequences long enough/usable to blast
Purple KS 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 Media:WFPurple260worksheet(updated).xlsx Media: WF260alignment-final.mas Media: WF260Tree-final.pdf
Purple AM 260 Short sequence Media:WFPurple260C5.txt Media:WFPurple260Overview.xlsx
Silver MO 252 Media:WFSilver252C1_v1.txt Media:WFSilver252C3.txt short reading poor quality Media:WFSilver252C_v1.txt no forward primer, not used Media: _TR252Excel.xlsx Media: TR-252-Alignment_finalv1.mas Media: TR-252-Tree-finalv1.pdf
Silver SW 252 Media:WFSilver252C1B.txt short sequence, not used Media:WFSilver252C2B.txt Poor quality Poor quality Media: _TR252Excel.xlsx‎ Media: TR-252-Alignment_finalv1.mas Media: TR-252-Tree-finalv1.pdf
White JRI 260 Media:WFWhite260C1.txt short sequence no priming short sequence no priming Media:WFWhite260C6.txt‎ Media:WFWhite260C7.txt‎ Media: WFWhite260C8.txt Media-_TR252Excel.xlsx‎ Media: WF260alignment-partial.mas Media: WF260Tree-partial.pdf
White CTC 260 Media:WFWhite260C12.txt Media:WFWhite260C13.txt Media:WFWhite260C14.txt Media:WFwhite260.xlsx Media:WF260alignment-final2.mas‎ Media:WF260TreeFinal2.pdf‎

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



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