Metagenome＠KIN User Manual ver2.01
Contents
1. LC Metagenome KIN Edit Help Ctrl4 M Mew Analysis Switch Workspace Export Active Chart or Table Export All Charts and Tables Preferences a ww sc EXIT Rie chart Ma rank In order to export all data in a project select File gt Export All Charts and Tables Once your select a stored location all graphs in HTML tables in CSV and cluster analysis results will be exported Following information will be exported bk 01 log J 02 hits result A 03 data table 04 pie chart y 05 sunburst chart A 06 data frame 07 bar chart Lk 08 pca 2d A 09 pca animated 3d A 10 pca interactive 3d A 11 cluster heat map i 12 self organizing map User Manual Version 2 01 Metagenome KIN File Edit Help Pan jouer E ee v di BlastTest2 Y Classification analysis EJ RL4 1 RL4 2 1 RL5 1 Statistical analysis analysis log file Assigned bacteria name table for each read Frequency analysis result table for each ranks pie chart image and pie graph source data in CSV sunburst graph image in html Frequency analysis result table throw all samples bar graph image in html and bar graph source data in CSV 2D PCA analysis result image 3D PCA analysis result image auto frame by frame 3D PCA analysis result image manual frame by frame hierarchical cluste2. www w fusion coa jp kin users 7f958iltw OQod5r4n5 urslag php On the license authorization page enter the followings User name Organization name Email address and physical address MAC address of the computer A license file will be emailed to the entered email address from World Fusion The software will be available by selecting KIN license from the file Select a license file You need to register to obtain a license file by visiting our website at https www w fusion ca jp kin users 7f958i bw OQod5r4n5 urslog php Choose a license file to enable MetagenometKIN Browse MAC Address 6C 88 14 33 96 50 User Manual Version 2 01 Metagenome Kin User Manual How to obtain physical address 2MAC address Method 1 MAC address of the installed PC will be displayed on the KIN license authorization window Type the numbers in the entry box on the license authorization web page Select a license file You need to register to obtain a license Tile by visiting our website at https w Www w fusion ca jp Kkin users 7f958i 1w OQod5r4n5 urslog php Choose a license file to enable MetagenometKIN Browse MAC Address 60 88 14 33 96 50 OK Method 2 For Windows open Command prompt and enter getmac Then MAC address will be shown F C Userstuser eetmac 10 User Manual Version 2 01 Metagenome Kin User Manual IV Analysis Execution from BLAST result IV I Analysis Execution
3. v CH BlastTest2 Classification analysis RL4 1 RL4 2 Qui STENT NI RR ASTA REA BA RL5 2 EJ RL6 1 E Fi LIII default em wm IIT T r rank you want to see rm em pm pm rem rm pm pm rm rm rem pm pm rem pm me F Statistical analysis 19 User Manual Version 2 01 Metagenome Kin User Manual IX Gluster Analysis Result Display In a case of analyzing multiple samples Metagenome KIN executes following 5 kinds of analyses PCA 2D Principal Component Analysis 2D PCA 3D Animation Principal Component Analysis 3D animation PCA 3D Interactive Principal Component Analysis 3D interactive Clustering Hierarchical clustering NUS SS SA SOM Self organizing Maps To view clustering analysis results select one from the pull down menu after selecting default under Statistical Analysis in the project folder Once you select a rank from the pull down menu its clustering analysis will begin Metagenome KIN File Edit Help v Hh BlastTest2 v ES Classification analysis 3D animated PCA 2 Select clustering I I RL4 1 3D interactive PCA analysis and rank_____ RLa 2 Clustering n SOM code info nnd SOM map plot RL6 1 RL6 2 statistical analysis sr cd E 1 Select default in I pm I S default Statistical Analysis 20 User Manual Version 2 01 X 2D PCA Analysis Result Display Selecting 2D PCA a 2D plot image for e
4. Metagenome Kin User Manual KIIN Metagenomee Kin Metagenome KIN User Manual ver2 01 Metagenome Kin User Manual Contact details World Fusion US Inc 4025 Camino Del Rio South Suite 300 San Diego CA 92108 TEL 619 542 7879 E mail techsupport w fusion co jp URL http www w fusion com All rights reserved under World Fusion US Inc No part of this documentation may be reproduced stored or transmitted in any form without the prior permission of World Fusion US Inc 2014 08 User Manual Version 2 01 Metagenome Kin User Manual Contents sg E Rede Reale es 4 I dnstall Mgr 5 IT Install SESDS EE 5 II JE mstallot hand BPClIDEAFIes cce p o ea nt na he s n e dede 6 ke EE UE I QVO EE 7 UE ED dn so 6 de EE 7 HE ECOSSE am n MM MAMMA IM Ex MM AM LAE EA 9 IV Analysis Execution from BLAST result esee tnter tnter treat tn enses 11 IV L Analysis Execution desc ate MEE I EL uc MM a bd 11 IV I Analysis Result Display d it E ote b E E Se eee 12 Mo PIS GHArtePallszueetentatedtdtn tet erste a std uo I Ld ILLI eL Ed dao iE ten 14 Vi C to e EE Cala cmm 15 VIL Analysis Result OUPS EE 16 M We FE gt ofl E E 16 VI II Save Location of Analysis Data Files ttt eee t eere e bae eat ee te bed rage tees 16 MEL Outputs of Analysis D EE 17 VII Bar Graph Display from Multiple Samples sentent 19 IX Cluster Analysis hesult DIsbladys
5. cz Click New and enter PATH as a variable name Enter the whole path Leg C Program FilesYRYXR 3 1 0XbinYx64 for R x64 into variable value In addition enter the whole path e g C XProgram Files R R 3 1 0 library rJava jri x64 to x64 under the jri folder of R library rJava after putting a semi colon Example is shown as below C Program FilesXRXR 3 1 0XbinXx64 C XProgram Files R R 3 1 0 library rJava jri x64 Set up a path to R library folder Click New and enter R LIBS as a variable name Next enter the whole path Leg C Program FilesYRYXR 3 1 0Xlibrary for R library folder in the variable value User Manual Version 2 01 Metagenome Kin User Manual New User Variable Variable name R_ LIBS Variable value xXProgram Files R R 3 1 library a Cos Click OK and finish the Environment Variables setting You can start the application created by the shortcut of Metagenome Kin on the Desktop MEtqqenOT NEN If you have any problems during the install process please contact our customer support E mail techsupport w fusion co jp User Manual Version 2 01 Metagenome Kin User Manual III License Demo license term is two weeks Following message will pop up when your demo license term has expired Open the shown URL on the message for a user authorization File Edit Help Software License Application has not been activated Please register at https
6. Select New Analysis using BLAST from File tab The following analysis start menu will be displayed T4 Metagenomeag KIN am a Edit Help Mew Analysis Using BLAST Ctrl N Mew Analysis Using RDP Switch Workspace Export Active Chart or Table Export All Charts and Tables Enter analysis project name Required Metagenome KIN File Edit Help CH Testi Test bh Test3 EJ test4 LH Test5 Teste hb Test7 Project Name Description Filter Conditions BLAST filter conditions m i Identity 36 W Mismatches mi Alignment Length iX Gap Openings ix Bit Score 3 A E value im Include number of rejected hits read trapped read by BLAST filter im Include number of no BLAST hits read e value gt 0 001 Reset Filter BLAST Results Files drag and drop files allowed Add Files BLAST result files Cancel anis D P ed You can alter the filter conditions for BLAST results Once you click Reset Filter it goes back to the default setting Identity the lower limit of the sequence identity alignmentlength the lower limit of the alignment length bitscore the lower limit of twice the length of homologous local alighnement mismatches the number of non matched bases gapopenings the number of base gaps e value the upper limit of the e value After setting the filter condition drag and drop BLAST result files on the input area Multiple files can be
7. shows each microbe and each arc s angle is the same The difference of pie diameters correspond to a component ratio of sample microbes which construct its pie Therefore pies in a circle and adjacent circles have similar sizes and color Pies in a SOM circle list top 14 microbes have big dispersion between samples big distributions between samples Self Organizing Map Code Information Self Organizing Map Mapping Plot Class Class Mer of H i d i RL5 2 RL5 1 i T i TZ NM d a N r MN gi Ts a En f pra ba BR Ka Je Se SS ee x Fa Ki d fb i VG oy f 1 1 i FO f a d X s d 2 fal fa e Em e md er o e Bs ME r Ex D E T WS rdi A Fl V pH x d L d 4 d X J w VJ A Rig 2 RLE 1 RLA 1 nai H J T D k d A i i d r i A ef i Ao P 1 d itt mod i Be amp ridnharteriia Chlamydia Gammaproteobacteria ene We Aclinabaderia Clastridia Ha amp iphaprateabacteria Deinocnpcci Mitrnspira Bacilli Deltaproteabaclerna Sphingobacteriia Betaproteohacteria Flavobacteria You can export a SOM analysis result image in a PNG format from the Export function in File menu 24 User Manual Version 2 01 Metagenome Kin User Manual XIV Metagenome Analysis for Reads who Do Not Pass Blast Filter Conditions 11 77 1 By checking boxes of Include number of on analysis execution menu you can analyze reads which do not pass the filter conditions from BLAST resu
8. the analysis Menu folder CSV file Spreadsheet data for each rank Pie chart is created from this data Choose a workspace folder to use for this session Your analysis results are stored in a folder called a workspace Browse Ji 01 log A RL4 1 DL 4 03 data table ko RL4 2 j 04 pie chart li RLS 1 A 05 sunburst chart A 06 data frame A 07 bar chart Sample name HTML file Sunburst and Pie chart graph data your need FireFox to see the result accepted csv in 02 hits result folder Data of reads in which strain each read belongs to through metagenome analysis rejected csv in 02 hits result folder Excluded reads from analysis based on filter conditions no blast csv in 02 hits result folder Excluded reads from analysis based on BLAST setting User Manual Version 2 01 16 VI III Outputs of Analysis Data Metagenome Kin User Manual Graph data such as pie chart and sunburst graph can be exported by selecting File gt Export Active Chart or Table from menu The graph image will be a HTML document and table will be a CSV format Those data are available under FireFox and Excel In the case of the large number of microbes it is possible that pie chart and sunburst graph may not be displayed on the application In this case by exporting HTML results you can see the outputs on the web browser instead File gt Export Active Chart or Table FireFox will be required to see the exported image
9. zi E on pdf Step 4 exe p Guide pdf Select I accept the agreement and go to Next gt 4 Setup Metagenome Kin License Agreement Please read the following important information before continuing Please read the following License Agreement You must accept the terms of this agreement before continuing with the installation I accept the agreement I do not accept the agreement lt Setup Metagenome amp Kin cole Ready to Install Setup is now ready to begin installing Metagenome Kin on your computer Click Install to continue with the installation or dick Back if you want to review or change any settings Destination location C XProgram Files x86 Metagenome kim Start Menu folder Metagenome akin Additional tasks Additional icons Create a desktop icon ses I ea User Manual Version 2 01 Click Finish to finish the installation e Setup Metagenome kKin Metagenome Kin User Manual Completing the Metagenome Kin Setup Wizard Setup has finished installing Metagenome Kin on your computer The application may be launched by selecting the installed icons Click Finish to exit Setup Launch Metagenome kim II II Install of R and R libraries Install R and R libraries You have downloaded Metagenome Kin zip archive contains R installer and R libraries Double click the R installer as below and follow the instruction showing on the window as defaul
10. Superking IcIIHCQ JEGO CZK 583345 Meth 359408 Methyloter 359407 Methyloter 32011 Methylophi 206350 Methylophi 28216 Betaproteo 1224 Proteobact 2 Bacteria Icl HCQ JIEGO1 D3X NA NA 881957 Bacillus sp 1366 Bacillus 186817 Bacillaceae 1365 Bacillales 91061 Bacilli 1239 Firmicutes 2 Bacteria Icl HCQ JIEGO1 BSA NA NA 667502 Bacillus sp 1366 Bacillus 186817 Bacillaceae 1365 Bacillales 81061 Bacilli 1239 Firmicutes 2 Bacteria Icl HOQ JIEGO1 EP NA HA 454662 Cellvibrio s 10 Gellvibrio 135621 Pseudomor 72274 Pseudomor 1236 Gammaprot 1224 Proteobact 2 Bacteria Icl HCO JIEGO1 AWC NA NA 1096000 Stre pto myc 1883 Stre pto myc 2062 Stre pto myc 2037 Actinomyce 1760 Actinobacti 201174 Actinobacti 2 Bacteria Icl HOQ JIEGO1 DNTNA HA 1097711 Bacillus sp 1386 Bacillus 186817 Bacillaceae 1385 Bacillales 81061 Bacilli 1239 Firmicutes 2 Bacteria 18 User Manual Version 2 01 Metagenome Kin User Manual VIII Bar Graph Display from Multiple Samples In order to analyze multiple samples multiple BLAST result file at the same time the microbial construction of the all samples can be shown in bar graphs Clicking default under Statistical Analysis on the sample display area bar graphs will be displayed selecting Bar chart from pull down menu and proper rank Additionally each cluster analysis result is also available from the pull down menu gt Metagenome KIN 2 s E o a e File Edit Help CH BlastTesti 2 Select Bar chart and arcad I I I
11. a local Blast program When upgrading Metagenome KIN database you may need to upgrade the referred database as well for BLAST execution 1 From a download site in current database file mdb file presented by World Fusion you download and unzip a updated file for Local BLAST and switch the new blastdb folder from the old blastdb folder in the local BLAST program 2 Open blast txt in the folder where Local Blast is located Then edit the Blast database version name in the section of Blast DB The version number should match as the number in the blastdb folder blastdb S blast txt EUM Ee UH BLAST Parameter Hii _ ddbj 16s r96 nhd it Blast DB ddbj 16s r96 nhi ddbj 16s r96 nhr I hlas M LC a _ ddbj 16s r96 nin blastdb ncbi sbbct r 20 1 ddbj 16s r96 nog blastdb ddb 16s r94 _ ddbj 16s r96 nsd it Blast Program ddbj_i6s_r96 nsi ddbj 16s r96 nsq blastpe blastn i ncbi_gbbct_r202 fasta E ncbi gbbct r202 log _ ncbi gbbct r202 nhd ncbi gbbct r202 nhi Blastdb showing its database version in Blast txt needs to be changed c GREC NUR ii to Blastdb ncbi gbbct r202 _ ncbi gbbct r202 nin ncbi gbbct r202 nog and Blastdb ddbj 16s r94 _ ncbi gbbct r202 nsd _ ncbi gbbct r202 nsi _ ncbi_gbbct_r202 nsq Example If updated blastdb folder is constructed as left 26 User Manual Version 2 01 Metagenome Kin User Manual XVI Ref
12. ach microbe will be displayed The in the image indicates the information amount of PC1 and PC2 in the plot You can alter the rank display and export the 2D PCA analysis plot image from the Export function from File menu User Manual Version 2 01 Metagenome Kin User Manual 2D PCA Species 21 Metagenome Kin User Manual 3D animated PCA N XI 3D PCA Analysis Result Display Principal Component Analysis Species 99 6 Selecting 3D animated PCA a principal component analysis in 3D animation plot for each microbial level will be created 02 03 O4 0 1 pc3 0 0 Selecting 3D interactive PCA a plot of principal component analysis in 3D will be displayed However this 3D plot does not work on Metagenome kin application 0 4 0 3 02 0 1 0 04 03 02 01 00 01 02 03 04 Instead you can use FireFox in order to view the 3D Start Rewind Play amp Stol End Current position interactive PCA by exporting the file arti Rewin n urrent position Then you can modify angles and the size of the plot How to export 3D interactive plot On the menu File gt Export Active Chart or Table A html file will be created and it will be available under FireFox 22 User Manual Version 2 01 Metagenome Kin User Manual XII Hierarchical Cluster Analysis Result Display Hierarchical clustering result will be displayed by selecting Clustering from the pull down menu Highest frequen
13. added Click Submit to start analysis 11 User Manual Version 2 01 Metagenome Kin User Manual Once the analysis starts each entered BLAST file name will be displayed as its sample name in a folder under the entered project name with Classification analysis folder Analysis process will be completed once Complete the number of entered samples of the number of entered samples as shown below Metagenome KIN d File Edit Help Created 2014 08 05 11 15 21 Fay hb BlastTesti v Rn BlastTest2 ES Classification analysis Name RLA 1 BlastTest2 3 RL4 2 Analysis sample Description Analysis log i C RL5 1 Processing 6 out of 6 Start 2014 03 Reading and parsing RL6 2 bln done Input records 191955 rows Rejected hits 35628 Accepted hits 2695 Writing rejected hits to a file dane Writing accepted hits and taxon list to files done Elapsed time 4 4 sec End 2014 03 Completed 6 out af 6 IV II Analysis Result Display On the left side of the analysis window Pie chart Sunburst graph spreadsheet as analysis results will be displayed by clicking a sample name You can switch result graphs and hierarchical ranks from Mo rank the pull down menu on the light side of the window Pie chart Species Spreadsheet Sunburst Graph Family MetagenmeeKIN we WE Sf ow gr emm mm con xX File Edit Help gt CH BlastTest1 v H BlastTest2 v Class
14. cy will be colored in red and medium is yellow and lowest is white on the analyzed sample Clustering correlation average Class Color Key I Tree structure of similarity between gt E uw i Row Z Score I I samples i I E structure of similarity frequency between microbes Buc Se eee E I Chlamydia Detaproteobactena Sohingcoedie ia Closvidia acnotazsena Doltapectecbacteria Gammapicnsohariena phaprcteodscsna Venuoom oacbioe A ccckacecina Neggliviouies Gem atimzo adea RLA 1 RL42 RL61 RLE fy Ke x You can export the clustering analysis result image in a PNG format from the Export function from File menu 23 User Manual Version 2 01 Metagenome Kin User Manual XIII SOM Analysis Result Display A result of self organizing map will be created by selecting SOM code info or SOM map lot from the pull down menu A SOM clustering result file consists two clustering image files code png and map png for each classified level SOM map plot on the right shows clustering result information for samples and SOM code info on the left shows microbial structural component for each rank pie On a SOM map plot samples in the same circle have similar microbial components and there is similarity between samples in flanking circles SOM code info concretely addresses what kind of microbe is used for similarity On SOM Code info an arc color in a circle
15. erence Principal Component Analysis and Clustering I An R and S PLUS Comparison to Multivariate Analysis by Brian S Everitt 2005 Springer Self organizing map Self Organizing Maps by Teuvo Kohonen 2001 Springer Application of multivariable statistics for 16s RNA metagenome data Liu B Faller LL Klitgord N Mazumdar V Ghodsi M et al 2012 Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease PLoS ONE 7 6 e37919 doi 10 1371 journal pone 0037919 27 User Manual Version 2 01 Metagenome Kin User Manual XVII Current Functional Limitations Limits for license issuing Metagenome KIN is only available under an installed PC with proper physical address MAC address from a provide license file If a PC does not have a network device you cannot use the software due to unavailability of proving the physical address Limits for 3D interactive PCA graph display Due to JavaFX specifications used in Metagenome KIN graphic designs you cannot control 3D interactive PCA results In order to be able to control changes of display angles by drag amp drop or sizes of the mouse wheel you need to export the 3D interactive PCA graph in html format and see the result by FireFox 28 User Manual Version 2 01 Metagenome Kin User Manual XVIII How to Uninstall Control Panel gt Uninstall a program under Program and select Metagenome KIN 29 User Manual Version 2 01
16. genus species no rank the number of hit reads will be displayed in order from its center to the outside 15 User Manual Version 2 01 Metagenome Kin User Manual ViI Analysis Result Outputs VI I Spreadsheet Display Spreadsheet describes microbial frequency for each sample The frequency the number of read is hierarchically classified Rejected reads indicates the excluded number of reads through filter conditions from analysis execution n Metagenome KIN pull down menu File Edit Help hn BlastTesti Ch BlastTest2 Classification analysis Taxon Name Weissella RL4 2 Bacillus RL5 1 Enterococcus RL5 2 Pediococcus Senn Nocardioides 1 Clicking a sample its spreadsheet will Rejected hit be displayed VI II Save Location of Analysis Data Files 2 Select Spreadsheet and a rank from Spreadsheet Genus Y Taxon Count 1904 1027 336 239 235 30951 MetagenomeQKIN analysis data automatically create a folder sample name in the project name folder to store results as shown below File gt Switch Workspace The saved location directory can be modified select a workspace E Metagenome amp KIN New Analysis Ctrl 4 N Switch Workspace C AUsersXuseriworkspace Export gt A MetagenomeAnalysisl1 1 02 hits result gt Project name workspace Following analysis data will be stored each sample folder under
17. ification analysis RL4 1 RL5 1 Select sample to display RS b 2 CJ RLe 1 RL6 2 gt 3 statistical analysis gt dj RDPTesti gt CH RDPTest2 Pie chart Genus v Weissella Bl Pediococcus E Pantoea B Arthrobacter Stenotrophomonas 53 Janthinobacterium Lactobacillus User Manual Version 2 01 I Bacillus Streptomyces B Nocardioides Massilia BE Microvirga Lysobacter B Mycobacterium Enterococcus Nl Pseudomonas E Enterobacter P Rhizobium Bradyrhizobium I Acinetobacter Metagenome Kin User Manual You can delete each analysis project result by selecting the project and clicking Delete Analysis on Edit tab Metagenome KIN 13 User Manual Version 2 01 Metagenome Kin User Manual V Pie Chart Details k E BlastTesti Bs BlastTest2 ERA Y eg Corynebacterium 540 Fie chart b Genus Classification analysis F RL4 1 EJ RL4 2 xj I i i i RDO Clicking a sample name its pie chart will RL6 1 LjRL6 2 be shown ES Statistical arlatysig CH RDOPTestl d Ich RDPTest2 14 User Manual Version 2 01 Metagenome Kin User Manual VI Sunburst Graph Details Species Acinetobacter sp I Sunburst graph places superkingdom phylum Moving the mouse pointer the microbe and class order family
18. lts and unregistered reads in database Description Filter Conditions e Identity 4 gt 98 0 im Mismatches lt 1 i Alignment Length O im Gap Openings xe Y E Bit Score gt 0 0 L i E value lt 1 0E 30 at Include number of rejected hits read trapped read by BLAST filter m i Include number of no BLAST hits read e value gt 0 001 By checking Include number of rejected hits read trapped read by BLAST filter reads as Rejected Hits which did not pass filter conditions at KIN analysis execution can be displayed on graphs or clustering analysis By checking Include number of no BLAST hits read the number of reads from microbes which do not have phasic cut off conditions of BLAST execution will appear as No BLAST hits on graphs or clustering analysis A case of reject hits in analysis a case of no BLAST hits in analysis 20 User Manual Version 2 01 Metagenome Kin User Manual XV How to Upgrade 16SrRNA Database Metagenome KIN contains database of microbial names for Blast result files From a download site in current database file mdb file presented by World Fusion you can upgrade your database by switching the mdb file in rsrc folder within installed Metagenome KIN folder as shown below Metagenome Kin rsrc gt Z i L images _ 16sv3 mdb accepted html accepted_class html accepted family html In case that you ve obtained your BLAST result from
19. ring result image SOM analysis result image 17 Metagenome Kin User Manual Contents of bar chart folder amp bar chart 1 no rank html bar chart 2 species html bar chart 3 genus html d3 v3 min js SL dataframe 1 no rank csv Bar graph source data for each rank microbial frequency RE dataframe 2 species csv information of reads for each analysis sample lL dataframe 3 genus csv Bar graph image data for each rank FireFox is required Contents of pie chart folder pie chart 1 no rank html pie chart 2 species html pie chart 3 genus html lL datatable 1 no rank csv lL datatable 2 species csv El datatable 3 genus csv frequency information of reads for each analysis sample Pie chart graph source data for each rank microbial Contents of data table folder data table 1 no rank csv data table 2 species csv Table which microbe has how many numbers of hits from BLAST for rank Elj data table 3 genus csv Contents of hits result folder E No blast hit reads that did not satisfy filter conditions from BLAST execution accepted csv i Sms rejected hit reads that did not satisfy Blast result filter conditions from L no blast csv rejected csv metagenome analysis execution Accepted hits Table which read belongs to which microbe for each rank Query ID is the read name and Taxon ID and microbial name will be displayed for each rank Query ID No Rank Species Genus Family Order Class Phylum
20. s de qe et aa vete eere neret ever be d leet eee 20 X 2D PCA Analysis Result Display ossia eet onis aen rr testi antt reci iu rescate ev eec a tcn 21 AL SD PGA Analysis Result e E 22 XII Hierarchical Cluster Analysis Result Display eese 23 AIL SON Analysis Result EE 24 XIV Metagenome Analysis for Reads who Do Not Pass Blast Filter Conditions 25 XV How to Upgrade 16SrRNA Database 1 esent teretes ttti tees nn 26 AVE Te 21 AVI Curent Functional EE 20 PV AM FOW TURNS EC EE 29 User Manual Version 2 01 Metagenome Kin User Manual I Outline Metagenome KIN 16S rRNA Analysis Tool provides following results by inputting BLAST result files v Rejected Information information rejected by filters containing names of reads and the number of reads Pie Chart Sunburst Graph Bar Graph Principal Component Analysis 2D Principal Component Analysis 3D Animation Principal Component Analysis 3D Interactive Hierarchical Clustering Self organizing Maps SOM SN IN Sa er Nc UNS US User Manual Version 2 01 Metagenome Kin User Manual Il Install Windows I I Install Steps Decompress Metagenome Kin zip archive you have downloaded and double click the WF MtKIN2 0 0 exe installer D KH em d T D A gt a E Metageno Unzip R library WF MtKI License First jdk Bu5 wi R 3 1 0 wi DE M2 0 0 ex f Certificati Analysis ndows x6 n exe me kKin
21. t It will be usually installed under the folder C Program FilesYRYXR 3 1 0 5 R 3 1 0 win exe After the R installation transfer all the R libraries to the R library folder R R 3 1 0 library 7 Drag amp Drop Qu Program Files R R 3 1 0 library Ji base Ji boot i class d cluster r codetools User Manual Version 2 01 2014 06 06 15 07 2014 06 06 15 07 2014 06 06 15 07 2014 06 06 15 07 2014 06 06 15 07 A gdata m bitops Jb caTools A animation Ji gtools Am Jb scatterplot3d bam I gplots kohonen 1 ava Metagenome Kin User Manual II III Install of Java Obtain the Java installer from the following link Java http www oracle com technetwork java javase downloads index html Double click the Java installer as below and follow the instruction showing on the window as default 4 jdk Bu5 windows x64 exe II IV PATH Setting Set up a path of the R library in order to execute R on Metagenome KIN Open Control Panel go to System Advanced system settings and click the Advance tab and click Environment Variables The following window will pop up Enviranment Variables Liser variables Variable Value TEMP C Documents and Settings TMP C Documents and Settings New JD ee Y System variables Variable Value New User Variable Variable name PATH Variable value Program Files R R 9 10 library r Java b d
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