User Manual
Contents
1. Cancel the computer will ask you if you would like to create a blank lineup 3 If you selected Yes to creating a blank line up fill in your sample names or numbers into the middle column Once you have entered the Lineup win dow you will see three columns 4 LANE left column To select all samples click on Lane and the whole column will be highlighted To select specific samples hold the shift button while you select your samples 5 SAMPLE NAME middle column Enter your sample names here The of samples you name should correspond to the of lanes you select in the next step 6 TEST right column If you have several samples amplified using the same set of primers or primer group you can create Loci Rules to make evaluating your data easier In this column select the primer groups used for each sample In order to change more than one sample at a time select the lane of the sample in the left column then directly select the primer group in the right column All of the samples selected should follow suit In this case we choose to evaluate all our samples with the Locus Rules for primer group Equine 1b See the Locus Rules section to find out how to create your Own Page 7 ii Nand 2240 3 HH E He m Whee Hali n Saude Oh Pil GE iti am pees Pei Sa a Gel File HE ubone dhe randami 2241 Leet Filg BE NEAUNA Geretes TFF adeno SRPMS CMDS 120 _J Micron lt M Dansant LJ2. gt Loci rules Click the Add Test button Enter the name for the species or analysis that you will perform on your gels and click OK 2 Add locus rules Select the new test name and click on Add Locus New Locus Mame Shark Range 96 to 124 Example allele or M l 102 Allele Names 0 Letters O Number Translation w None Repeat Unit f gt Blue OK Cancel This is simply an example locus rules can be set using the locus rule tool pictured here or programmed manually in the locus rules window The Process is covered in detail on Page 10 and virtually everyone uses the locus rule tool because it makes life easy Repeat this process for each of the loci that you will want to score within this test group e g a species primer set or a specific analysis Color Se ee E E E E E E E E E E A E E A O E E A E E E E a E E E A E E 3 EXIT STRand we will want to incorporate the changes we just made 4 Restart STRand 5 Reset preferences Tools gt preferences Make sure that the value for Default configuration includes the full range of dyes for which you just defined locus rules and change it to the appropriate instrument and dye set configuration 1f it is not already there Click on the value for Default test and change it to the test you just named that includes your specific locus rules that you want applied to your gels and the size standard that you are using Page 5 Ente
3. unlike the image above If not in the Peaks box highlight each standard separately like in the example next page to make sure it corresponds to the correct peak on the electropherogram If a peak shows up that is not a standard but is being read as one you can block the program from recognizing it by right clicking in the left column of the Peaks box 6 Alerts If when you open DNA Type and the Gel Image box says Alleles before first standard you may need to readjust your included scans in the initial import of files Page 3 so that each lane includes your standards as well as all your amplification bands The Electropherogram Window il on iu 20000113C In the Samples column select then sample lane you would like to view Once you hl O Pe Ue Ll JU LLL TA Oe UULU L id ii have it selected the Electropherogram will 2 LIBF2 gi a0 is 110 rm 120 140 150 180 w io WO mo Ho 220 FM Mo MO 280 270 no ma mo Ho I display the results for that specific lane Graph Controls allow you to toggle each color marker on or off by simply double v 13603 2006 g EEHEHE HEHH clicking The X and Y zoom will allow MKO 7000 Dine assess you to stretch a selected peak horizontally r RE MT pe ALIE TI or vertically This box also contains a 12 it pH muin ag puu legend for the color coding for each dye aa i nii labeled primer e g TAMRA is represented by black peaks Gel Image shows th
4. 750 aE Ld aL 8 several things a es MHA q 24 MITS1E3 ue FBR Adding a peak the program has h Conio af Mask Typ Tyoe Sip Sie _ Heigh Label missed If you see a peak but it does ak eoig are coer RE cos ca a 5 fr Hed i ka 1G i ISN SE not register in the Peaks box you can ee IEZ 177783 17748718353 E 00 00 G01 Garnes manually select it by holding shift HMS 175101 175093181 14 Ga 00 976 Genesi Sve PS bo Gane clicking and dragging across the top of ata it This will add a size standard peak when no locus is selected or when a i BP Caa 242 997246 00 locus is selected a peak in the color of ee eS that locus Marking or Unmarking an allele of an existing peak If you see a peak and Basic Export of Allele Calling Data it is not registering as an allele of the selected locus right click on it and its bp 1 You can use the built in ResultViewer program see Page 15 to manage your data or you can do a simple size should appear in the DNA type box ER pOT Saa Also use right click to unselect a wrongly 2 While in the Electropherogram on the Toolbar click File Export Data called allele 3 The program will automatically tell you how many of your lanes have problems because of no size standards invalid alleles more than two alleles etc you should have already gotten a warning about this when working with the files on your gel image and mark
5. Progam Files Ci pstors Stone LJ noe S24 CIWDOD wS STRand Would you like to create a blank line up FERA Name 1 horse 1 2 horse 2 Equine 1b 3 horse 3 s Equine 1b 4 horse 4 Equine 1b 5 horse 5 Equine 1b a 6 Lane 6 Equine 1b Finding the Lanes you your Gel Image Again if you are using a capillary machine there is no need to find lanes on your gel so you can skip this entire page If however you are using slab gel system STRand needs to know where each sample is located on the gel and the find lanes process is 1 With your gel highlighted in the Gel Queue window click Find Lanes and a picture of your gel should appear If no picture appears in the Lane Find window check that the gel you are trying to analyze is the correct gel image file and not the ABI run file 2 To select the lanes you want to view double click in the middle of each single lane while holding the shift key As you double click a numbered line should appear 1 corresponding to the first lane you selected 2 to the second and so on The number of lanes that you find should correspond to the of samples in your lineup To delete a lane hold the shift key and right clicking on one of the nodes white dots 3 Adjust the lines so that they lie in the middle of the corresponding lane by moving your cursor over either end joint of the lane until a two way xd arrow appears Click once while moving the arrow in the desired d
6. delete nodes by holding the control key and right clicking with your mouse The left box of the gel file window allows you to view the vertical slice of gel corresponding to the highlighted line e g lane 15 is selected and we can see that it passes cleanly through all the size standards and a band 120bp Use the Lane Find Settings Window to change the settings of your gel picture Adjust the brightness by moving the tab and clicking Apply To automatically use the Find Lanes function adjust the height and delta to specify how many scan lines represent a real band and the least amount of scan lines between two bands respectively we actually find it easier to just find all the lanes manually like explained in steps 2 5 Use the Scale Image functions to stretch or shrink the gel picture for ease of viewing when selecting lanes To Analyze amp View Your Samples l With your gel highlighted in the Gel Queue window click DNA Type and an electropherogram of your gel should appear When your gel data is loading the program may say some lane data missing Just disregard and click OR This happens when you have less lanes selected than what your matrix allows e g only 90 samples but 96 wells allowed If when you first open DNA Type and in the Gel Image box it says No Standards Found you may need to reanalyze the gel Reanalyzing the Lane you can reanalyze just the lane itself by cl
7. off by right clicking in to a wedge that you can click on the peak the left column of the Peaks box and split it into two peaks some strong 5 The Gel Image box shows a virtual gel and the lane that you are currently viewing use the RETURN key alleles with a weak adjacent allele can be to move down from one sample to the next in the Samples box detected as a single fat peak 6 Use the SPACEBAR to move between markers of one sample on both the Electropherogram and DNA The Peaks box displays all the peaks Type box that are visible within the selected lane 7 The x axis of the Electropherogram corresponds to the bp length and the y axis corresponds to the For each peak there is also a peak scan height corresponding scan length base pair size 8 The ruler corresponds the specific marker highlighted in the DNA Type box The range of the ruler peak height and color label The red corresponds to the range set in the Locus Rules selected when creating the Lineup see next section Setting up Locus Rules L 9 In either the electropherogram window or the Gel Queue window click Tools and then Loci Rules Maximize the window so that you can see the Add Test and Add Locus Buttons To add a new group of primers click Add Test and enter the name of your primer group With the name of your primer group highlighted click Add Locus and a New Locus box will appear Name fill in the na
8. them with an asterisk You can choose to cancel 1 e go back and fix those lanes or ignore continue If you do not get this message all of your data checks out properly 4 If you choose to continue you will need to pick the number of lanes to export generally you want to do all of them but if you want the data from the first 10 lanes you can specify that 5 An Export Results box will then appear and you must specify where you want your data file to go and name it Once it has been saved you can view or print the results by opening the file in Excel Changing the size of a called peak If you think the program is calling a peak the wrong size you can change it by clicking on the peak and then clicking on the size that you think it should be on the drop down dotted line of range ruler im Sample Selection Sample amaa In order to view a specific sample that is located in several gels in a gel folder you can use Open Case to select specific samples to view together a gt Viewing Select Samples from Different Gels Together samplel Pc l o 24 00 Gel Fil sampled Pc l Sxsx 2 24 00 Gel Fil Remove 1 In the Gel Queue window click Open Case and a window like one below will appear 2 Type in the name of the sample that you want to view and click Add The Sample List will ag show all the gels that contain that sample Use Remove b
9. 1 Kd J Fr eee se Pai P i it j ir so l j Fill il it _ dom A i ij g n j cad Y DRS OTAD ele ee E ET A SS ee eS ye re ee Me EE bs ResultViewer Tools gt Result Viewer Seia Singe Gel Gel Hame Fisi ho aaa Im E NM O LT2 C BTHO LTI Sam of Empty types gal mem Uneuniad li fl L Los T Separste runs M Slhow bene boua F Shon haghi iy Lit Gel Group fo Type Anais i Marker Sis Min Gel hame eae tt fe Dry aiki bom Deia gets Ae UERHURAUBRREES Moho ERE RE SEE m Pa i ELF 160 ch 0 1a EIL Tha a 180 Pita im aoe T a 0 Tal A Wg 180 Fi a0 oa 180 Tu Pal Pas TAD Fa TE ae T Bc BoB The ResultViewer window will launch and you have the option to examine results from a Serial selection of lanes a single sample or an entire gel at once Type in the name of the gel from your Gel Queue and click Add Highlight the name of the gel and click on the Show button at the bottom of the window This will generate a table with the sample names listed down the rows and the loci listed across columns The first allele is listed in the column labeled with the locus name e g Pc102 and the second allele is listed in the following column Samples highlighted in red have an alert associated with them in the original gel file and missing data is represented by a zero 0 entry Scrolling the mouse cur
10. A Type to analyze your gel If you ever need to adjust your Loci Rules you will have to exit and re enter for any changes to take place See the next page for information on adjusting a pre existing locus The list of alleles control which alleles are listed in the chooser lines on the Electropherogram and what labels are assigned to each of the called alleles What everything in the Locus Window means i 2 Tests lists all of the existing primer groups or locus rule sets Size Standard make sure the size standard selected for the locus cor responds the standards used during ABI sequencing run Loci lists all the loci in the selected primer group Highlight a loci of interest to view its parameters Channel corresponds to the color designation of that locus primer Blue e g 6 FAM Channel 1 Green e g VIC Channel 2 Yellow e g NED Channel 3 Red e g PET Channel 4 Purple e g LIZ Channel 5 Allele Info In the Allele Info box are the expected sizes of the sequence for the primer from the smallest to the largest spacing between the numbers a comma then a space then semi colon e g 122 124 126 and so on If you input even numbers the machine will round even and odd numbers will round odd In this example we expected an even di nucleotide repeat so we can get away with inputing the sequence sizes spaced two bps apart 7 Analysis Script Rounding Script an
11. Veterinary Genetics Lab STRand Version 2 2 30 Copyright 1996 2000 Regents of the University of California Written by Melissa Locke Eric Baack amp Rob Toonen University of California at Davis 2000 Updated by Rob Toonen June 2007 Copyright 2000 2007 All rights reserved Quick introduction to STRand Software Basic Program Operations Page 2 Setting up STRand amp user preferences Page 3 Starting STRand amp importing your files Page 4 Creating Locus Rules Page 5 Entering STRand amp creating Gel Groups Page 6 Adding gels to your Gel Queue Page 7 Creating a gel Line Up Page 8 Finding lanes on a slab gel not for capillary machines Page 9 How to Analyze and View your samples Page 10 The Stuff in the Electropherogram Window Page 11 Setting up Locus Rules Page 12 What everything in the Locus Window means Miscellaneous Useful STRand Information Page 13 Selecting and Unselecting peaks Exporting Data Page 14 Comparing Samples amp Superimposing Lanes Page 15 ResultViewer and Upgrading STRand Setting up STRand software A Downloading and installing The most recent version of STRand is on the UC Davis VGL Home Page at http www vegl ucdavis edu informatics STRand B Setting up STRand once installed The updated version of this manual assumes that users do not need to create a matrix file or dye standards for their machine If that a
12. d Globals The Analysis and Rounding Script boxes contain pa rameters for calling and estimating peak sizes based on the information in the Globals box The Globals box contains the specific parameters for that locus the same ones that you i Rand ZAW Lon Fades 4 af Fie Tios Mew Wride Hele CO ede E x gune Ip Venice ORC Chore n Hiti mrm m o 4 do dolce Ab ee er lang eel a Fini Ges peat Leighi Loi this locus Vexeaqge of foe i 1 te Laer Peake Coane ce Rese one Lae Praks 2 3152 Lf i Lane rabipi Plangeplese ami E Mavilesqae Lase Peake si anant mia ii sent Fi iter fe ight hog Tones ela eg ne kom work Clrouh peak and apply fiiveia Esc b 1 co Lapp Peaks COELI ie Pe iy ral Filcerhear yir sekire E ira Eije a J m aaa e i i 0 7 mee Fus r ound rg Mapt THmctaon Rois ace Pain gedtare iLagi ffasce B ce Fepiinit POURS S1 fe Pines 1 te Coy Rep init m O LagiClagif T Pom aoSa ne Pnenetat Found Finizaiest te End Punt ion Bom ASSRE RD lesiteczz _ Finink ELI SOUTH SO pom defined when creating the locus Move Up Move Down The Move Up and Move Down buttons will change the order of the primers within a primer group The way that they are ordered in Loci Rules will determine the order in the Electropherogram window during your analysis ie Ham rt ome STA Tf you ever need to make adjustments of your locus param
13. dd your gels to your new gel group as follows 1 Select your gel group in the lower right hand corner of the Gel Queue If you have just created your gel group you should not see any pre existing gels in your folder 2 Click Add Gels and select the file that contains your gel The ABI Sequencer outputs three files after its run a gel file a log file and a run file The gel file contains the gel image that you will want to analyze 3 As you are selecting a gel to add you also want to select the appropriate instrument that your gel was run on e g ABI 377 A 96 can be used if your gel was run on an ABI 377 and has 96 lanes You may need to manually add a matrix file and instrument configuration if none of the available instruments fit your needs 4 Once you have your gel selected click Add and your gel should automatically be added to the Gel Queue window File Toke View Window Heb U Gel Qunwe Pol Sxx 2 24 00 Gel File Poot Stor 00 Gel File ranma ADI 377438 Creating a Line Up for your Gel This is done automatically if you followed the instructions on Page 3 but if you need to change or add a line up you will 1 Once you have added your gel highlight it by clicking on it once 2 Click Line Up and the computer will ask you to select a file that contains your lineup If you already have a lineup created in a text document you may select that or by clicking
14. e actual gel and the lane that you be ie I Ls i MA p Ul j are currently viewing 20 MH391 Je o kea of uh Al aa hn The DNA Type box allows you to view eee uber 40 10 16 2 i 480 gon 640 Gi BAO FE 00 79g a00 840 oa oda 1H AIH MAHA hth bakti hh i your data according to the Loci Rules specified in the Lineup Each Marker corresponds to a primer and the program 3 TE PETTE will automatically estimate the size of any f m HME OPN 167 169 16746 16952 peaks within the range and color specified I TAMRA HHS Lo 477 17748 18353 for that primer see below to set up Loci RG jn _ EAL KE on Rules In this example primer ASB2 7 evaluates any FAM colored peaks between 222 258bp The blue peak that is highlighted is a heterozygote with two peaks one at 246 and one at 248 Type corresponds to either the letter or size designation Pressing Z or BACKSPACE corresponds to GeneScan standards and in this example the 300bp standard is highlighted both in the Peaks box as well as on the electropherogram Sometimes the program will read peaks that are a result azas 1 mig ri i I Ga il F i 1 r m F al 8 C Loe LE Tr LLI ITI z i pi L i i i r 5 if E E sS un r ue ore I la aa i j Lay yy t acs W 06 IE na moves you back one marker Selecting a peak and pressing V changes the pointer of pull up or stutter that you want to disregard These peaks can be toggled on or
15. e color of the traces dye labels that you prefer the default path to the folders in which you keep your gel files and so on The important things to set are a Default configuration this must match the general sequencer platform even if the exact model number is not available and the complete dye set that you are using In our case we have an ABI 3130XL which is not included in the default list but the ABI 3700 FVNPL 6 FAM VIC NED PET amp LIZ option is equivalent and works just fine for analyses b Default size standard this should match the size standard that you are using to score your alleles but can be changed in the test that is applied c Default test this is the set of locus rules and the size standard that you want applied to your samples in order to score the allelic sizes once you set locus rules Pg 4 The rest of the settings under preferences can be considered personal preferences but these three settings must generally be set correctly in order to score your data For example you can specify the directory from your data will be imported and where you will want results exported These can be the same directory but they don t have to be 8 EXIT STRand we will want all the changes we have made to take effect Page 2 Importing a gel from the sequencer to STRand 1 Start STRand 2 Add sample files File gt Add Sample Files Use the explorer window to navigate to the folder in w
16. eters you can do it manually by changing the information in Boxes 1 7 For example say in the primer group and locus above your max range expanded to 150bp and the color of your primer was actually green not yellow First in the Allele Info box add sizes 148 and 150 spaces with a comma space or letter designation and a semi colon 142 L 144 M 146 N 148 0 150 P Next in the Globals box change RangeMax to be 150 M your standard allele to set binning to be 146 and Plane same as Channel to 2 Lastly change Channel box to read 2 as well STAand 2 2 11 Miscellaneous Useful STRand kerim e 100 110 120 120 140 160 180 170 180 190 200 210 20 20 Mo M0 200 27D 200 NO We 210 10 Selecting and Unselecting peaks in the Electropherogram pe The program based on the Locus Rules we will call any normal alleles in the locus oo paitane range For example in the picture on the 000 hrenin i right locus ASB 2 is selected and its poe 0 Been i range ruler is visible The program has 1 MH307 nt i See called this peak a heterozygote with a 246 ca alter a i 1 Vi id ee and 248 allele But if you believe the D9 MH39111 Eag AL AJ RI g m A ee AR es A MH35112 ii per fi A S Thik Ip S O AN KEE KEE A L l automated calling is in error you can do p Seas ET per acer eRe iasaid A AANAND GAA Saahid Rhdbe La BR AAA SDAAAANESAA Alden vial hi eee w i i ati Li O aL aia al An OOO amp I TO Fe Be BA Bi Be Te Tn eo ee
17. hich your samples from the sequencer are stored on your hard drive It is important to include only sample files from the sequencer in that folder because other files can confuse STRand a OK Cancel Starting Scar 3000 Ending Scan IS on iw Append Tube E Add Sample Files Aun Name 6 6 05 toby ABI Sf 00 FYAIPL j Select samples to load Instrument Ei Select All Double check that the instrument matches your dye set and set the run name to something that will make sense to you a year from now when you have 100 gels to go through in order to find this one Click the Append Tube and Autonumber boxes to include all the samples in your folder and automatically create a line up see Page 7 for you otherwise you will get unnamed samples that stop at the same number of samples as your machine has capillaries The Starting Scan allows you to cut off the front of each sample The default starting scan of 3000 is sufficient to cut off the unincorporated primer fronts and generally gives a cleaner electropherogram but can be reduced if very small fragments need to be scored To be safe this value should initially be set to O and increased to an appropriate starting point after looking at a number of gels Generally a value close to 3000 is about right Click OK when ready 3 Check the settings Double click on the name of the gel run name in the gel queue to check that the configuration s
18. hown is the one you expect instrument configuration and dye set Change to the correct one 1f needed This is also where you can delete the gel results if you decide that the calling was incorrect and you want to start over e g with a new configuration 4 Analyze the gel Click on the run name in your gel queue window to highlight it and click on the DNA Type radio button to analyze the gel files This may take a moment with many lanes of data but you should see the progress moving along steadily on the screen 5 Check that the number of samples matches your expectation if you ran a 96 well plate but only have 16 samples here or don t have any names associated with your samples you most likely forgot to check the Append Tube and Autonumber boxes when adding sample files Also check to make sure that the spacing on the alleles 1s consistent and that the marker names match your locus rules that you have set see below Any of these being off is a sign that something has gone wrong with the automatic gel analysis or you have made an error in the configuration when adding your sample files Page 3 Set up locus rules for your gel analysis You will want the lanes on your gels to be scored according to the appropriate locus rules that you have determined If you are working with multiple species or multiple people are using the same computer you will want unique locus rules for automatic size calling of each locus 1 Tools
19. icking Lane then Analyze on the toolbar Changes will happen immediately Reanalyzing the Gel If all the lanes require reanalyzing it may be easier to just reanalyze the entire gel On the toolbar click Window then Gel Queue Double click on your gel and a Gel Settings win dow should pop up It should not be necessary unless you have changed something with rounding or loci rules but if you need to click Delete Results then Yes and reenter the Electropherogram by clicking DNA Type or Window Your Gel File Once you are back into the Electropherogram on the toolbar click Ge and Analyze You will lose any previous data but 1f this is the first time you are analyzing your gel you should have no data yet to lose ELE H Standards nol lowed na i 5 J p 1b La ER 41 biar E 17 Lana FS 12 Lape Ela TE Lae Ee 15 heme BPS Ti Leer Ele 1 Lome Bis Te Liane ET 7E Lone Pa ECinstesvers i f a Lra RO l thy l Fl TNI BETEN mp l EEPE UU UL LP ie ee Allelas before first standard ITI Lee HT l W012 Lare Ui 8 13 Lore 13 14 Laa Hii 15 L e His 16 Lana HIT ane 5 Checking your Standards Once the program recognizes your standards you may want to make sure the peaks correspond to the correct bp size The simplest quality check is to make sure that the spacing is consistent and covers the appropriate size range
20. irection To get the best readings make sure that your line passes through all of the size standards red bands for that lane 4 You can also adjust the top red line and bottom green line parameters by holding the cursor over line until a up and down arrow appears Drag and drop so that the bottom line green cuts out the blob of junk and primer dimers if you fail to do this you may have problems getting STRand to read the standards correctly but leaves at least 1 and pref 7 erably 2 size standard peak s between it and the lowest band you intend to size The top line red should leave at least 2 size standard peaks above your last allele for best accuracy in size calling 2 Shift DBL cick bo select lanca to view beget fix Dela f i Fap ka oot ie hrama Ome s AML Lanas Prd Lares i al A ope N F ene Lat Nonig 5 CRTL DEL elick Sande lga E Sain bo fi lo crenle mew joni 3 Place curzo here to 4 Adjust top and bot gel e arrow for R L Lorn pereme wing ad justrent i If you can not get the line to match up with your lane by just adjusting the end it is possible to adjust along the length of the lane as well To reshape the line set the cursor where you would like the line to bend and hold the control key while double clicking A new joint will appear along with a two way arrow that can be moved either right or left You can also
21. me of your new locus or primer Range from min to max fill in the expected alleles sizes of your ampli cation Estimate a range based on a known peak size if you do not know the range you can always change it later when you know the range Example allele enter the standard allele to determine rounding of your allele sizes to odd or even the most common allele is a good choice Use Letters if checked this command assigns letters to each allele size e g 122bp A 124bp B 126bp C Repeat Unit corresponds to the ex pected repeat size in bp e g CACACA is a2 unit repeat CATCATCAT is a 3 unit repeat Color choose the color that your new locus primer is tagged with 10 Repeat steps 3 through 9 until all your loci have been added DASARATA 18 x a acs a a Hem loc ngra peas i Faroe lO ret es Emcee akiaja hi ao Ue Leen s Add len Pichi F wra AENEA Eina flew Pul Fima ian w EAS R E You can evaluate several primers within one group so add as many loci as you need to your primer group This is most effective if you make new primer groups for each multiplex PCR being evaluated Once you have finished setting up each locus within your primer group close this window and your Loci Rules will be ready to use Ifyou select the appropriate test primer group when first importing your gel files it will automatically be applied when you click DN
22. ring STRand ter 1 Open the STRand program and the STRand Login window should pop up 2 Click Manage Once in the Manage Users window click Add Type in your name 4 Click OK and then Done Your name should now be added to the STRand Login window Click once on your name then click OK to en ter the program a You should now see this screen the Gel Queue Currently the only folder available to store your gels is in Equine Production If you want to create your own folder Gel Group see below Lanes found Ana I To create your own Gel Group Equine Producton monkeys 1 On the toolbar click Tools Manage and Gel Groups 2 In the Gel Groups box all current gel groups are displayed and to add yours simply click Add 3 Inthe Input Window type your Gel Group Name and click OK 4 For STRand to activate your new settings EXIT the program and re enter 5 Once you ve returned to the Gel Queue window your new Gel Group can be entered by clicking on the down arrow in the lower right hand box and selecting your gel group Once you have created your own gel group you can then add and analyze your gels If you are using a capillary sequencer your gels are added by following the instructions on Page 3 so skip the rest of this page If you are using a slab gel machine you need to a
23. sor over any entry cell will give a pop up widow of the metadata underlying that calling gel lane locus alleles called etc so that you can go back to the DNA Type window and locate the sample to double check the calling The complete table can then be saved directly as an Excel data file dat or as a text file for import into whatever spreadsheet program is preferred Upgrading STRand to the latest version without overwriting your existing data If you want to upgrade your working version of STRand to the latest version you can find your STR mdb file usually in c program files strand and copy it to a temporary folder Download and install the latest version of STRand as outlined at the beginning of the manual and then copy your STR mdb file back into the STRand folder overwriting the one you just installed This process will transfer all of your existing data into the new version of the software
24. ssumption is incorrect and you need to configure your instrument manually refer to the original version of the instruction manual for the information STRand configuration files are stored in an Access database found in the STRand directory Microsoft Access is not needed for normal use of the program However you may wish to work with the files directly if you run into a bug Note Updating the STRand preferences and configuration is an iterative process in other words you usually need to exit the program and restart it for the changes that you have made to take effect in the STRand program 1 Computer environment Change your display settings 1f needed to at least 1280 x 768 resolution lower resolution can result in program difficulties 2 Start STRand and choose a user name 3 Create a gel group for your data or one for each set of data as this will keep things organized Tools gt Manage gt Gel groups Add Enter the name for each unique gel group or folder of fsa files that come off a capillary sequencer that you wish to keep separate in your analysis Done ee Note We ll say it again updates are iterative so the gel groups window in the lower right corner of the screen will not show your new gel groups until you have exited from STRand and then restarted the program from the newly modified database 4 Verify that your sequencer is identified Tools gt Preferences Here you can set th
25. y selecting any samples that you do i not want to view and click Remove 3 Once you have finished click OK and an Electropherogram will appear that only contains the lanes specified oF Cancel Superimposing Lanes in a Multi Lane Electropherogram If you have two lanes in a gel that you want to view one on top of the other you can use the Multi Lane Electropherogram function 1 Inthe Electropherogram click View and Multi Lane Electropherogram A Lane Selection box should pop up 2 In the Lane Selection box click under the lanes of interest select the dye color of the peaks that you want to superimpose In this example I want to see the blue peaks all together from lanes 2 7 and 10 Click OK and the MultiLane box will appear 3 On the left of the MultiLane box it lists all the dye colors possible for the lanes that were selected The dye colors designated by a full colored box are shown the half colored boxes are not All lanes selected for the same dye color will be represented by a different shade for ease of viewing e g since only blue was selected for lanes 2 7 and 10 they are shown as blue for lane 2 purple for lane 7 and pink for lane 10 The X and Y switches will shrink or stretch the image horizontally or vertically respectively Lane Selechon 1415 16 17 18 2 x aT root d Tadi 7 2 Pet 7 MH 90s mit Mm mH390 bei 10 MASS 10 TA z 12 10 MH39
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