What`s new - JSI medical systems
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1. 14 What s new SEQUENCE Pilot 4 0 0 2 1 Version 4 0 0 1 1 All modules 1 1 1 SEQUENCE Pilot screen The SEQUENCE Pilot screen has a new layout 1 2 Modules SeqNext SeqPatient and SeqC 1 2 1 Operation Sequence Alamut interface An Alamut interface for mutations is available now Therefore enter the following entry in the lis ini file located in the bin directory of your installation Section SeqPilot MutationSendExtern send to Alamut http localhost 10000 show request JSIDATA There will be the context menu item send to Alamut available for mutations in the Variation Mutation table then Moreover in the Alamut software the following setting has to be changed menu Tools Options register option enable HTTP access has to be activated 1 3 Module SeqNext 1 3 1 Operations PCR Products PCR Groups and Enrichment master file These operations are not available any longer The operations PCR Products master file and Enrichment master file were combined in the new operation ROI master file ROI Regions Of Interest The operation PCR Groups master file was renamed into Groups master file Note All enrichments and Multiplicom MASTR assays have to be defined newly for version 4 0 0 1 3 2 Operation ROI master file ROI stands for r2. eae ens 9 even ett ent er ener het 9 1 3 6 2 Files Groups Genes Chromosomes 5 9 ae eee Rie 9 1 3 6 4 6 9 136 9 10 1 3 6 6 Pseudo Electropherogram 10 T Be 10 E E E E 11 Context menu for combined forward and reverse 11 4 Tool tip for combined forward reverse 11 Fragmani VEN airen n EE EEEE E 11 Lone oe R EA PEET 12 bo Er NEENA E TTA reel 12 1 4 Module SeqHLA 454 13
3. 5 SEQUENCE Version 4 0 0 and 4 01 07 20 2012 a SEQUENCE JSI Pilo te medical systems BE GmbH www jsi medisys com 0015 is M goal Ge efi Laer of LTT TT aa TT T CARRA ANDET A ao a a 1 E 1 tt ae Tt ee 220177 0 ZUTATEN developed by JSI medical systems GmbH JSI medical systems Corp Friedhofstr 5 1901 Newport Blvd Suite 350 77971 Kippenheim Costa Mesa CA 92627 GERMANY USA phone 49 7825 863620 0 phone 1 949 999 2092 fax 49 7825 863620 20 fax 1 949 999 2093 email mail jsi medisys com email mail us jsi medisys com web www jsi medisys com for research use only Table of Contents 5 4 4 SEQUENCE Filol SEGG i 4 1 2 Modules SeqNext SeqPatient 5 4 1 2 1 Operation Sequence Alamut 4 Mone arora E EE EE E
4. Use this tab to define PCR products as done former operation PCR Products master file the new field State new is pre selected Therefore only ROIs that were just added not saved yet will be listed in the ROI List After saving the list will be empty To see all defined ROIs select the State blanc 1 3 2 3 Tab add Enrichment Note All enrichments have to be defined newly for version 4 0 0 For orders analysed with older versions single ROIs in the RO Location table of the operation Sequence can not be recalculated Use this tab to define Enrichments The entry in Amplification can have up to 24 characters and should define enrichment chip e g SureSelect or NimbleGene The entry in Suffix can have up to six characters The suffix is added to the Name of the ROI e g Suffix ng for NimbleGene ROI name is BRCA1E01 ng Therefore ROIs added on tab Enrichment have a suffix in the ROI name listed in column Name There is the setting auto cut available If you use this setting the sequence is cut to the entered values for each ROI e g setting is 5 20 and 3 30 All ROIs are cut to 20 bases before the exon and 30 bases after the exon in case the sequences defined on the enrichment chip are longer The settings auto complete check equal cut primer and combine are not available any longer In the new field State new is pre selected Therefore only ROIs that were just added not saved yet will be li
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6. Amplicon parts are defined in the operation RO s master file see chapter 8 3 1 2 Fragments that do not cover the complete Amplicon part are discarded barcode at both ends only for 454 lon Torrent data Choose this setting in case barcodes have to be present at both ends of the fragments Fragments with only one barcode are discarded Remove bases a number of bases that should be removed at the 5 at the 3 end can be entered into the corresponding field Adaptor sequences can be entered to trim or discard fragments e g for Haloplex or Fluidigm Adaptor 5 gt 3 Press Then enter an adaptor sequence in 5 gt 3 direction Only active adaptors will be removed The following fields can be edited for each entered adaptor Direction forward adaptor is found in forward fragments reverse adaptor is found in reverse fragments both adaptor is found in all fragments o Modifier 5 trev complement primer is at the 5 and can also be found rev complement 5 primer can be found at the 5 end only complement primer is at the 3 end and can also be found rev complement 3 primer be found at the 3 end only Count here a value can be entered in case an adaptor is present several times Error rate here a percentage value can be entered as error rate wrong bases that the adaptor can contain Overlap Here the minimim number of adaptor bases that must overlap with the
7. Extras gt and select deactivate gene The mark in the column Active of the Genes table is then removed A gene can be activated again by pressing Extras gt and selecting activate gene In case several isoforms should be active a hierarchy can be set up The isoform on top is always the main isoform To set up a hierarchy for active isoforms use Extras gt gt change gene With the arrows you can change the order of the isoforms When Amp Modules and are defined the main isoform is used first For all exons that do not exist in the main isoform the next isoform in the hierarchy is used When loading files and more then one isoform is active and no Amp Modules Seg Primers are defined first the loaded files are checked with the first active isoform If not all sequences can be aligned the second active isoform is checked and so In the Positions Resultfiles table the used isoform can be seen in the column Loc In case not the main isoform is used there is an index behind the location e g 2 means that of the second isoform was used 2 2 2 Operation User A user who has no right to edit masterfiles can not edit Gene Admin as well 2 3 Modules SeqPatient SeqHLA 2 3 1 Operation Sequence Edit Bases In Edit bases the count modes AA amino acids and cDNA are available now What s new SEQUENCE Pilot 4 0 0 12 The jumper check gt statistic is available to jump to positions with stati
8. SEQUENCE Pilot 4 0 0 5 1 3 4 Operation 1 3 4 1 Files bam and sam files can be loaded now for paired end sequencing data several groups of files can be imported now 1 3 4 2 Settings The settings have been changed Profiles including special settings can be saved and selected in the field Profiles e g different settings for different platforms Moreover the fragments can be trimmed either by entering Adaptors e g for Haloplex or Fluidigm or by automatically removing sequences at the ends of the fragments Using the Settings button the dialogue Settings can be opened to adapt settings 1 Coverage settings Coverage f r separated The coverages in forward and reverse sense are considered separately A mutation is only listed in the Variation Mutation table if the coverage reaches the required coverage in forward and reverse direction In case the coverage is regarded separated all absolute values e g Min absolute coverage are also regarded separated This setting is recommended to use when coverage in sense and antisense is about equal and high enough f r combined The coverages in forward and reverse sense are considered combined mutation is listed in the Variation Mutation table if the coverage of the mutation reaches the required coverage compared to the total coverage at the position In case the coverage is regarded combined all absolute values e g Min absolute coverage are also regarded combin
9. fragments are shown or if fragments above a certain coverage should be shown To see all fragment sequences you can open the fragments view as usual The bases can be highlighted in different colors o insertions deletions have a blue background Deletions are indicated by a minus sign Inserted bases are shown if you move the cursor over the position o mutations listed in the Variation Mutations table have red background likely basecalling errors which not listed in the Variation Mutation table have an orange background When you scroll through a location using the horizontal scroll the vertical scroll is moved automatically to show the fragments sequences for the current position Insertions deletions are shown as red arrows pointing upwards for insertions and downwards for deletions above the pseudo electropherogram For a better overview the gene sequence first green line is expanded for distinct insertions there is a sign at the inserted positions The distinct insertion is included in forward reverse and combined sequence What s new SEQUENCE Pilot 4 0 0 9 Positions with coverage below Min absolute coverage can be set ih operation Run Settings are visualized in the combined forward and reverse sequence in the following way by greying out the sequences individually Example 1 coverage in fwd lt MinAbsCov but gt rev gt grey out fwd Example 2 coverage gt MinAbsCov in
10. AA TE 4 1 3 1 Operations PCR Products PCR Groups and Enrichment master 4 kag TIE 4 4 6 EMCE 6 Toda ToD 230 1 gerbe pepe eg pcs yw eves ecg 6 1 3 3 Operation Groups master 6 ices es ice eel coe ov an sa is osetia 7 ee eee T i E a Tea Mert eee ener err ene 7 T Govorno SeMS inner nE REEERE EERE EEE 7 2 Settings to trim or discard 5 2 0 8 tcc cpt tect beset ao nr ge ce acne secede ee steer ego vane eo ee 9 9 1 3 5 Operation Joining Worklist and Archiving Select 9 GR
11. ToSNP default is 3 for the maximum number of bases between two SNPs DelInsGapSNPToInDel default is for the maximum number of bases between a SNP and an Insertion Deletion or between two Insertions Deletions If the gaps between variations are within the thresholds InsDel is created which summarizes the variations into one to be shown as InsDel in the mutation table 2 5 1 2 Alignment If you want to see all fragments aligned to the reference even if the alignment is bad e g fragments of a highly mutated virus you can switch off all quality filters by adding the following entry to the lis ini file UseFilters no within the SeqNext section What s new SEQUENCE Pilot 4 0 0 13
12. and Groups master file can be selected The tabs Auto Search Gene and Auto Search Genome are not available any longer 1 3 4 4 Buttons The button Analyse was renamed into Start analysis 1 3 5 Operation Joining Worklist and Archiving Select Orders The search fields PCR Products and Enrichments are not available any longer ROIs can be selected in field ROI 1 3 6 Operation Sequence 1 3 6 1 Orders For old orders that were not recalculated with version 4 0 0 no settings are displayed 1 3 6 2 Files Groups Genes Chromosomes ROls Locations The context menu item reanalyse is not available any more 1 3 6 3 PCR Groups The dialogue PCR Groups was renamed into Groups 1 3 6 4 PCR Products Locations The dialogue PCR Products Locations was renamed into RO s Locations New context menu items e editing gt o recalculate recalculates the location o gettings opens the dialogue Settings to change the settings for the location After What s new SEQUENCE Pilot 4 0 0 8 changing settings the location is recalculated automatically show gt ROI Info Information about the ROI such as Amplicon parts Primers Ignored Sequences and Ignored Parts can be edited 1 3 6 5 Variation Mutation table The tab low coverage is not available any longer A new radio button is availalbe to decide if mutations are listed for all genes or for the gene selected in the dialogue Genes Chromomoso
13. ed This setting is recommended to use when coverage in sense and antisense is different and not high Distinct coverage the percentage coverage of a base reaches at least this value the mutation will be listed on tab distinct of the Variation Mutation table The percentage coverage is the coverage of a base divided by the total coverage at this position times 100 Ignore coverage If the percentage coverage of a base is below this value the mutation will not be listed in the Variation Mutation table Therefore all base changed with a coverage below this value are regarded as likely basecalling errors If the percentage coverage of a base is between Ignore coverage and the Distinct coverage the mutation will be listed on tab other of the Variation Mutation table Min absolute coverage This value refers to the absolute coverage at a position Sequence positions with a coverage below this value are written in grey instead of black Mutations variations at those positons are not listed in the Variation Mutation table In case separated coverage is used and the coverage one sense 15 below the Min coverage absolute only the sense with the coverage above the Min coverage absolute will be regarded For those mutations the column Coverage of the Variation Mutation table is marked pink In case the coverage is regarded separated and there is a mutation in one sense with coverage above the Min absolute coverage whereas the other sense i
14. egions of interest This operation combines the operations PCR Products master file and Enrichments master file All regions of interest can therefore be defined in this operation Tab all ROI gives an overview about all defined regions of interest Selecting tab add PCR enables definition of PCR products tab add Enrichment enables definition of enrichment chips and tab add Kit enables the definition of kits such as Multiplicom MASTR assays In case a single region of interest has more than 10000 bases the region is splitted into smaller regions automatically A warning is then shown 1 3 2 1 Tab all ROI The RO List lists all defined regions of interest enrichments and PCR products In the new field State you can choose new ROI Then only ROIs that were just added not saved yet will be listed In the new field Amplification you can choose an amplification Then only ROls where this amplification was used are listed The amplification is shown in the column Amplification of the ROI List For PCR products the entry is PCR automatically for Enrichments and Kits it is user defined e g Roche NimbleGene Agilent SureSelect or Multiplicom can have up to 24 characters What s new SEQUENCE Pilot 4 0 0 3 Moreover the column ROls added tab add Enrichment tab add Kit have a suffix whereas ROls added on tab add PCR have no suffix e g BRCA1 E01 ng Enrichment 1 01 PCR The following new fie
15. er 5 gt 3 Only active primers will be removed The following fields can be edited for each entered primer Direction fwd primer is found in forward fragments rev primer is found in reverse fragments both primer is found in all fragments o Modifier 5 trev complement primer is at the 5 and can also be found rev complement 5 primer can be found at the 5 end only complement primer is at the 3 end and can also be found rev complement 3 primer be found at the 3 end only o normal PCRs where a primer is the beginning at the end of each fragment the following entry should be used Direction fwd Modifier 5 rev complement and Direction rev Modififier 5 rev complement o Error rate here a percentage value be entered as error rate wrong bases that the primer can contain This can be done seperately for 5 and 3 end o Overlap Here the minimim number of primer bases the fragment must contain can be entered Example overlap is 3 There must be at least 3 primer bases found in the fragment otherwise it is not trimmed This can be done seperately for 5 and 3 end o case the primer is not in the end of the fragments an area where the primer is searched for can be defined as follows ATGCTC 10 This entry means that the primer ATGCTC is searched for in the first 10 bases of the fragments What s new SEQUENCE Pilot 4 0 0 4 1 3 2 2
16. fragment can be entered Example overlap is 3 There must be at least 3 adaptor bases found in the fragment box trimmed discard trimmed is selected the fragment sequences are trimmed adaptor is cut off If discard is selected all fragments containing an adaptor are discarded Moreover there is a function available to automatically remove sequences at the ends of the fragments e g adaptors that do not match to the reference Remove ends The user can decide to remove bases at the 5 and or 3 by activating the What s new SEQUENCE Pilot 4 0 0 7 box For removing ends number of bases beginning from end of the fragment to number given in the field Distance is checked o Incase there no mismatches nothing is removed o Incase there are mismatches it is checked if sequences start to match within the Distance area In case a match is found the matching sequence must have at least the length entered field Blocklength can include as many mismatches as entered the box Max mismatches The bases before for 5 or behind for 3 the first matching base are then removed Incase there is no matching block found nothing is removed The platform settings are not available any longer the platform is determined automatically 1 3 4 3 Tabs The tab RO comprises the former tabs PCR Products and Enrichment Here regions of interest pre defined in the operation ROI master file
17. ft mouse button Button Filter Opens the Fragment Filter window you can filter for fragments that fulfill special criteria When OK is pressed only those fragments will be displayed in the fragments view There are several options o mark a position a fragment in the fragments view and select the context menu item add to filters The Fragments Filter window opens automatically In the table you can select the direction fwd rev both that should be filtered Moreover you can select invert or normal in the column nvert With normal all fragments that have that base at that position will be shown with invert all fragments that do not that that base will be listed o moreover several options can be activated complete paired end for paired end data only only sequence pairs where fwd and rev sequence is present are shown hide BC errors fragments with basecalling errors are not displayed Quality Filter for fragments above a certain quality score enter 1 100 Count Filter for fragments that are above a certain coverage count o filter is removed by right clicking the entry in the table and pressing remove when the fragments view is closed when another location gene and so on is selected New button X Y scroll to switch between two scroll modes for the X and Y scroll In case this button is pressed the scroll is always moved in X and Y direction default setting In case the button is no
18. fwd AND rev gt grey out fwd rev and combined Example 3 InDel coverage lt MinAbsCov in fwd but gt in rev gt switch to combined and grey out if fwd rev lt MinAbsCov Example 4 insertion coverage lt MinAbsCov in fwd AND rev gt grey out fwd rev and combined Example 5 For heterozygous deletions bases are not greyed out in case the coverage is below the Min absolute coverage for the deleted positions only This visualization supports the fact that a read direction is not considered in the weighting of the base change insertion deletion if it is below the Min absolute coverage 2 New mutation type W A warning is shown for sequence parts that can not be assigned Those are listed in the Variation Mutation table the Type is W In the pseudo electropherogram the positions are marked by arrowheads pointing left for reverse sense or right for forward sense As for all other mutation types warnings are marked red for distinct and grey for not distinct mutations The sequences can be displayed by opening the context menu right click on the arrowhead and selecting show fragments view or show Mutation 3 Context menu for combined forward and reverse sequence There are new context menu items available for combined forward and reverse sequence ignore sequence part This item can be used to ignore a sequence part For ignored sequence parts no basecalling is done Therefore first select a sequence part in the combined forward
19. he new field bases quality is selected only in case they are present in the Next generation sequencing file The quality score is visualised as an alternating colored line below each base There are five different colors available by default What s new SEQUENCE Pilot 4 0 0 10 dark green means good quality score close to 100 changing to dark red which means bad quality score close to 1 The selected base in the fragments view can be changed with a double left click on a base The base position is also changed in the electropherogram then Bases in the fragments view can be marked by pressing Ctrl and mark the sequence using the left mouse button With a single left click the selection is removed A sequence can be ignored in the fragments view using the context menu entry save as ignore sequence Sequences to ignore can be marked by pressing Ctrl and marking the sequence part with the left mouse button Sequences ignored here are listed in the field gnored Sequences Pseudogenes the operation master file There is the new context menu item add fo filters available With this a base can be added to the filter e g a base change mutation The new window Fragments Filter opens see below Button Filter There is the new context menu item copy gt sec selection gt sense antisense available to copy a selected sequence in sense or antisense direction To select a sequence press Ctrl and mark the sequence using your le
20. lds settings can optionally be adapted for each ROI Ignored Parts For Ignored Parts there is no basecalling done This function can be used in case there are parts of the ROI that are not sequenced Sequence parts can be ignored in the operation Sequence using the new context menu item ignore sequence part of the combined forward and reverse sequence Sequence parts ignored in the operation Sequence are listed in the following way position 1 position2 For the numbering the amplicon count mode is used remove an ignored sequence right click an entry and select remove from the context menu Ignored Sequences Pseudogenes Here sequences that should be ignored e g pseudogenes are listed All fragments the contain the here listed sequence are not used for analysis A sequence can be ignored in the operation Sequence in the fragments view Therefore mark a sequence in the fragments view using the Ctrl key and marking the sequence with you left mouse button Then open the context menu and select save as ignore sequence These ignored sequences are listed in the field Ignored Sequences Pseudogenes operation master file automatically remove an ignored sequence right click an entry and select remove from the context menu ROI Amplicon Parts Here amplicon parts can be defined This is usable for all platforms now Primer 5 gt 3 Press Add Then enter a primer sequence in 5 gt 3 direction into the field Prim
21. mes only New column Gene which lists the gene In the column Pos the absolute chromosomal postion 15 listed in parenthesis behind the position in the reference sequence New mutation type W is present for sequence parts that can not be assigned 1 3 6 6 Pseudo Electropherogram and Sequences 1 New layout The layout of the pseudo electropherogram sequences has been improved Defined amplicon parts operation ROI master are shown as red lines below the Location overview The coverage of the location is shown graphically below the Location overview In case the coverage is below the Min coverage line the graph is marked pink The pseudo electropherogram is shown for the combined sequence only Bars indicating coverage are shown separated for forward and reverse sense below the pseudo electropherogram light blue for forward and purple for reverse Fragment sequences are shown below The fragments sequences of the fragments in forward and reverse direction are listed Forward sequences are highlighted in light blue reverse sequences are written in italics and are highlighted in purple Paired end sequencing data e g MiSeq data are shown as pairs now overlapping regions are colored orange The number of fragments detected is shown in the beginning of each fragment For each amplicon amplicon part only the fragments sequences occurring with the highest coverage are shown It can be set in 1 5 how many
22. or reverse sequence Then use ignore sequence part to ignore this sequence All ignored sequence parts are shown in the operation ROI master file in the field Ignored Parts For numbering the ignored sequence parts the amplicon count mode is used gt for all items sequences be copied in sense or antisense reverse complement direction new item gt selection gt sense antisense copies the selected sequence to the clipboard 4 Tool tip for combined forward and reverse sequence Quality scores are shown behind each base in the tooltip only in case they are present in the Next generation sequencing file as an alternating colored mark There are five different colors available by default dark green means good quality score close to 100 changing to dark red which means bad quality score close to 1 In the tool tip for the reverse sequence bases are listed complement reverse 1 3 6 7 Fragments view The header of the fragments view now shows the ROI gene and exon plus whether it shows the reference or an InsDel The header is empty if an empty ROI is selected and the fragments view is still open On the new tab combined forward and reverse sense fragments are listed The combined sequence 15 highlighted light green Forward sequences are highlighted light blue whereas reverse fragments are highlighted purple For MiSeq data overlapping regions are colored light orange Quality scores are shown when t
23. s below the mutation will be marked pink in the Variation Mutation table This mark shows that the result is based one sequencing direction only Min coverage line Enter a value for the Min coverage line which is shown as a red dotted line in the electropherogram In case there are positions with a coverage below this value you will get a warning for the ROI What s new SEQUENCE Pilot 4 0 0 6 o There is the hint ow column Coverage of the table The graph color of the coverage graph below the location overview changes from grey to pink set fragments unique Only use this setting for special amplification methods For some amplification methods each fragment must have a coverage of only 1 If this setting is active the coverage of all identical fragments is set to 1 Genome Set Select if you use diploid or haploid DNA Homopolymer settings only for 454 lon Torrent data o Min homopolymer Default 40 Insertions deletions in homopolymer regions are listed on tab distinct of the Variation Mutation table if their percentage coverage is higher than the Min homopolymer value Otherwise they are listed on tab homopolymer o Homopolymer region size By default a homopolymer region is defined as at least five repeats of a base This setting can be changed here 2 Settings to trim or discard fragments compl fragments only only for 454 lon Torrent data This setting is only relevant when
24. sted in the RO List After saving the list will be empty To see all defined ROIs select the State blanc All other functions are the same as in the former operation Enrichment master file 1 3 2 4 Tab add Kit Note All Multiplicom Kits have to be defined newly for version 4 0 0 Orders analysed with older versions using Multiplicom kits can not be recalculated in the operation Joining and in the table of the operation Sequence Use this tab to define Kits e g Multiplicom MASTR assays The functions are the same as for Tab add Enrichment here the tsv file for Multiplicom Kits can be loaded instead of the files defining the enrichment 1 3 3 Operation ROI Groups master file The operation PCR Groups master file was renamed into RO Groups master file Here all regions of interest can be grouped In the field Amplification the amplification type e g PCR can be selected Only the corresponding ROls are then listed in the table below Multiplicom MASTR assays are not defined in this operatian any more they can be defined in the operation ROI master file using tab add Kit The tsv files and the fas files including the setup data for Multiplicom MASTR assays has to locate the folder SeqgNPart Kits Multiplicom of your installation now instead of SeqNPart Multiplicom For further details about the set up of Multiplicom MASTR assays please have a look at our User Manual for module SeqNext What s new
25. stic warnings in the dialogue Edit Bases 2 4 Module SeqgPatient 2 4 1 Operation Joining Result files with DNA number and defined Seq Primers that can not be aligned to a gene can be forced to be joined to an order now Therefore the entry JoinRFForced yes has to be entered in the lis ini file section SeqgPilot Then result file sequences that can not be aligned are automatically joined to the order depending on the DNA number for order and the Seq Primer for exon Result files that were forced to join have the entry forced join in the column State of the operation Joining In the operation Sequence those result files are visible in the Positions Resultfiles table and highlighted rose No sequences are shown since the result file sequence can not be aligned to the gene 2 4 2 Operation Sequence For every position resultfile a comment can be entered in the Position Resultfiles table Therefore select the context menu item show gt comments A new window opens where a comment can be entered The comment is saved by pressing OK Moreover it can be exported as txt file by pressing Save as 2 5 Module SeqNext 2 5 1 Operation Sequence 2 5 1 1 Variation Mutation table Base changes and insertions deletions that are close together not more than 3 bases in between by default are regarded as insdels Two values can be specified in the 1is ini section SeqNext to change to regard them as single mutations DelInsGapSNP
26. t pressed you can scroll in X or Y direction separated The button All Matches is not available any more To show matches only the new filter hide BC errors can be used 1 3 6 8 Report The report has been worked over 1 3 7 Operation Pool In the Variation Mutation table there is a new radio button is availalbe to decide if mutations are listed for all genes or for the gene selected in the dialogue part Genes Chromomosomes only like for the operation Sequence What s new SEQUENCE Pilot 4 0 0 11 1 4 Module SeqHLA 454 SeqNext 1 4 1 Operation Sequence 1 4 1 1 Fragments view The selected base in the fragments view can be changed with a double left click on a base The base position is also changed in the electropherogram then Bases in the fragments view can be marked by pressing Ctrl and mark the sequence using the left mouse button With a single left click the selection is removed 2 Version 4 0 1 2 1 All modules 2 1 1 Locking When a master file is locked by another user the name of the user will be listed in addition to the message that the master file is locked 2 2 Modules SeqPatient SeqC and SeqNext 2 2 1 Gene Admin Genes can be deactivated now Therefore they are not regarded any more when an autosearch is done Moreover they are not available any more to create Amp Modules and Seq Primers and they are not available any more in the Genes search fields of Select Order To deactivate a gene press
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