Batch Rename
Contents
1. Proxy Settings Check for Updates Figure 2 3 The plugin manager with plugins installed When you close the dialog you will be asked whether you wish to restart the workbench The plugin will not be uninstalled until the workbench is restarted2. Seq Replace full name With 2BR D RNA Seq BRE Press Shit F1 tor options 5 FZ Sequencing reads Figure 1 9 The entire name is removed from the primer names and is replaced with Today s date BR D the userdefined text RNA Seq and the addition of consecutive numbers BR E In this case we have inserted a space between the date the user defined text and the added number If commas were inserted instead the commas would be part of the new name as everything that is typed into the text field will be used in the new name when renaming the entire name CHAPTER 1 INTRODUCTION TO BATCH RENAME 10 Click Finish to start renaming Please note that the rename cannot be undone and that it does not show up in the History Chapter 2 Install and uninstall plugins Batch Rename is installed as a plugin Note In order to install plugins and modules the Workbench must be run in administrator mode On Linux and Mac it means you must be logged in as an administrator On Windows you can do this by right clicking the program shortcut and choosing Run as Administrator Plugins are installed and uninstalled using the plugin manager Help in the Menu Bar Plugins 2 or Plugins 3 in the Toolbar The plugin manager has two tabs at the top e Manage Plugins This is an overview of plugins that are installed e Download Plugins This is an overview of available plugins on QIAGEN Aarhus server 2 1 I
3. field are some of the most commonly used regular expressions Other standard regular expressions are als o admissible in this field Note Please ensure that if you choose any of these options or other regular expressions that you check in the CHAPTER 1 INTRODUCTION TO BATCH RENAME 8 box labeled Interpret From as Java Regular Expressions If you do not check this box then the characters you enter in the From box will be interpreted literally For example a full stop or period is interpreted as that character when this box is not checked but is interpreted as meaning any single character when the box is checked An example if you enter From Regular Expression Range A Z To Enumeration BR E titles containing any capital letters will be renamed to consecutive numbers A more advanced example where the sequences shown in the images earlier in this manual are used is shown in figure 1 8 The sequence names contain both a capital letter small letters and a number In the first the number is kept and a date is added in front of the number HEF Sequencing reads dri es arid 96 IE ear wd4 Replace part of name From 4 7 a z 2 To BR D _ Press Shift Fi for options Press Shift F1 fi options Interpret From and To as Java Regular Expressions 3 Sequencing reads Figure 1 8 The letters Fwd are removed from the primer name and replaced with Today s date In this
4. Batch Rename Plugin USER MANUAL User manual for Batch Rename 1 6 Windows macOS and Linux February 23 2018 This software is for research purposes only QIAGEN Aarhus Silkeborgvej 2 Prismet DK 8000 Aarhus C Denmark QIAGEN Contents 1 Introduction to Batch Rename 4 2 Install and uninstall plugins 11 Soe Wer pene E E eee aeeaebeueewe kee E 11 2 2 Uninstall eat oe ee we Ge a ws a a a ae ee ee oe 12 Chapter 1 Introduction to Batch Rename With the Batch Rename it is possible to rename your data in a batch fashion This will hopefully save you a lot of time when the names of your sequences and analysis results need to be changed To run the batch rename tool Toolbox Utilities x Batch Rename ale This will open the dialog shown in figure 1 1 where you can select the input data r g Batch Rename 1 Select Elements E SA Navigation Area Selected elements 9 CLC_Data a X6 Fwd1 gt Example Data mx Fwd2 7X ATP8al genomic sequence x Fwd3 7C ATP8al mRNA x Fwd4 i Translated to Protein Xc Fwd5 fht ATP8al mm Revi Genome Genome oe Cloning we Revs Primers ee Protein analyses Protein orthologs RNA secondary structure f Sequencing data XC ATP8a1 mRNA reference 4 Sequencing reads mou PIR RR RRR RRR oe w a a ot 3 gt gt Figure 1 1 Selecting the data you want to rename Click on the button labeled Next to go to the
5. case we have also inserted a space and a _ between the date and the number which was the only thing that was left from the original primer name Please note that in order to be able to remove both of the small letters in the primer name you have to add 2 which indicates that a z should be performed twice As this can be a bit difficult to grasp we will look at three more examples We will use the name 1N R1 0001 in the two first examples 1 First we want to keep only the first 4 none whitespace characters of the name s To do this write the following in the From and To fields shown in figure 1 8 From S 4 Nomenclature start of the line S none whitespace characters 4 4 characters everything after the pattern To 1 Nomenclature 1 the first group in the From field The result of this is that 1NR1 is kept whereas the space between N and R1 and _0001 have been discarded 2 If we would like to keep only the last 4 characters of the name s From 4 S Nomenclature x the first group 4 any 4 character at the end of the line as the second group To 2 Nomenclature 2 the second group in the From field The result of this is that 0001 is kept whereas 1N R1_ has been discarded CHAPTER 1 INTRODUCTION TO BATCH RENAME 9 3 Now we would like to replace the first letter followed by 9 numbers in the name p140101034_1R_ AMR with the parent folder name which in this case is Amert ca
6. ead mappings using Rename reads in mappings For read mappings there is also an option to Rename reference sequence in mappings E E Batch Rename L Select Elements E t pa aie iS gt 2 Filter Elements 3 Select Target Type Rename Target Figure 1 4 In this example we have four elements left As we only have one category represented in this case four primer sequences the other target type options are disabled Click on the button labeled Next to open the last dialog in the renaming procedure see figure 1 5 r g Batch Rename 1 Select Elements Serpe LAZE 2 Filter Elements 3 Select Target Type Rename Options 4 Select Rename Options Add text to name At the beginning At the end Replace partofname From To Replace full name With BRE Figure 1 5 Rename options At this step you can choose whether you wish to add text to the existing name replace some of the name or replace the entire name At this step you can select between three different renaming options For each text field you can press Shift F1 Shift Fn F1 on Mac to get a drop down list of advanced placeholder options The three options are shown in figure 1 6 along with the drop down list available for the first option e Add text to name This option will add text at the beginning or the end of the existing name depending on which you choose Pressing S
7. ename 1 Select Elements 2 Filter Elements 3 Select Target Type Rename Options 4 Select Rename Options Add text to name Press S 3 At the At the Replace partof name From E Inte Replace full name With mae Figure 1 7 Advanced options for The option to replace part of a name is bas hift F1 for options beginning end To Regular Expression Range A Z Regular Expression Union A D M P Regular Expression Intersection A P amp amp D H Regular Expression Excluding A M Regular Expression Subtraction A Z amp amp M P Regular Expression Any character Regular Expression Exactly n times X n Regular Expression At least n but not more than m times X n m Regular Expression At least n times X n Regular Expression Group expressions ABC Regular Expression Either one or the other AJB Regular Expression In the beginning of the sequence Regular Expression In the end of the sequence rename of only part of a name ed on regular expressions Regular expressions allows you to describe text in a flexible manner For more details please see http docs oracle com javase tutorial essential regex By clicking in either the From or To box a time Shift Fn F1 on Mac you will see nd pressing the Shift and F1 keys at the same a drop down list of renaming possibilities The options listed for the From
8. h a comma An example is shown in figure 1 3 Fs g Batch Rename 1 Select Elements _ Setparameters Input xx Fwdi xx Fwd2 xx Fwd3 x Fwd4 2 Filter Elements Filter Use comma to separate filters Exdude Rev 5 Indude Total input 9 Filtered 5 Remaining 4 e Previous ausDNertinns Y Erish iK canc Figure 1 3 In this case we are looking at primers The full list of primers can be seen in the previous figure In this figure the exclude function has been used to filter away all the reverse Rev primers as well as primers containing the number 5 In this case we excluded a forward primer Fwd5 The data that you will exclude are automatically removed from the list above the filters as you type in your restrictions This allows you to check the consequences of the added filters Click Next to go to the next step in the renaming of your data see figure 1 4 At this step you can specify at which level you wish to perform the renaming For a single sequence as in the example shown in figure 1 4 this is straightforward because it has just one name and you would use the Rename elements But if you have a sequence list for example you could choose either to rename the list using Rename elements or the sequences in the list using Rename sequences in sequence lists The same goes for alignments using Rename sequences in alignments and CHAPTER 1 INTRODUCTION TO BATCH RENAME 6 r
9. hift F1 Shift Fn F1 on Mac will enable a list of different renaming options as shown in figure 1 6 The different options are presented as e g BR E which means Batch Rename Enumeration the current name is kept and if At the end was selected consecutive numbers will be added directly CHAPTER 1 INTRODUCTION TO BATCH RENAME s g Batch Rename 1 Select Elements 2 Filter Elements 3 Select Target Type Rename Options 4 Select Rename Options Add text to name Replace partofname Staessen Current name of element BR CN Current name of element Short form BR CNS Latin Name of Sequence BR LN Latin Name of Sequence Short form BR LNS Description of Sequence BR DS Accession of Sequence BR ACC Parent folder filename BR F Name of Parent element BR PE Today s Date YYYY MM DD BR D Replace full name Enumeration BRE ERES ences gt o ven Ke Figure 1 6 Rename options for addition of text to an existing name after the existing name without introducing a space between the existing name and the new addition Please note that the numbering will follow the order of which the data were selected in the first dialog under Select Elements e Replace part of name This is an advanced function that allows to replace e g data with completely different names in one go with a new name This is shown in figure 1 7 r g Batch R
10. ion 1 2 Build 170222 1036 157093 Tools to analyse bisulfite converted reads Size 2 0 MB Sa Forward and reverse reads shaping a peak l Proxy Settings l Check for Updates Install from File Close Figure 2 1 The plugins that are available for download Select Batch Rename to display additional information about the plugin on the right side of the 11 CHAPTER 2 INSTALL AND UNINSTALL PLUGINS 12 dialog Click Download and Install to add the plugin functionalities to your workbench Accepting the license agreement Part of the installation involves checking and accepting the end user license agreement EULA as seen in figure 2 2 END USER LICENSE AGREEMENT FOR QIAGEN AARHUS SOFTWARE a Bisulfite Sequencing 1 2 0 W 1 Recitals 1 1 This End User License Agreement EULA is a legal agreement between you either an individual person or a single legal entity who will be referred to in this EULA as You and QIAGEN Aarhus A S CVR no 28 30 50 87 for the software products that accompanies this EULA including any associated media printed materials and electronic documentation the Software Product 1 2 The Software Product also includes any software updates add on components web services and or supplements that QIAGEN Aarhus may provide to You or make available to You after the date You obtain Your initial copy of the Software Product to the extent that such items are not accompanied by a separate
11. license agreement or terms of use By installing copying downloading accessing or otherwise using the Software Product You agree to be bound by the terms of this EULA If You do not agree to the terms of this EULA do not install access or use the Software Product 1 3 A static license to the software product allows the software product to be used locally on one specific computer system When using a static license only a single instance of the software product can be running at any given time 1 4 The software product is for research purposes only 2 SOFTWARE PRODUCT LICENSE 2 1 The Software Product is protected by intellectual property laws and treaties The Software Product is licensed not sold 2 2 You may install and use one copy of the Software Product on one single computer device workstation terminal or other digital electronic or analogue device Device 2 3 You are not licensed to do any of the following 2 3 1 You may not sell license or distribute copies of the Software Product on a stand alone basis or as part of any collection toroduct or serice of anw kind I accept these terms Cancel Figure 2 2 Read the license agreement carefully Please read the EULA text carefully before clicking in the box next to the text I accept these terms to accept If requested fill in your personal information before clicking Finish If Batch Rename is not shown on the server but you have the installer file on you
12. nSamples From A Z d 9 Nomenclature A Z any character as long as they are part of A Z a z the CLC software do not differentiate between upper lower case d 9 any 9 digit numbers the second group of the name anything after the A Z d 9 pattern To BR F S2 Nomenclature 2 the second group in the From field The result of this is that we have replaced p140101034 with AmericanSamples and as a result have changed the name from p140101034 1R_AMR to AmericanSam ples 1R_AMR 4 If we want to extract and use the text Sample code for the new name from the following 1234 sample code_56 78 with Java Regular Expressions From _ _ _ _ Nomenclature _ Starting from the beginning and match anything before the first underscore _ will match anything and stop before the second underscore After the second underscore the match will include the rest of the name To 2 Nomenclature 2 includes the match from the second group which is flanked between the first and the second underscore symbols of the name e Replace full name Allows replacement of the entire name with the name that is either typed directly into the text field or with options that can be selected when pressing Shift F1 Shift Fn F1 on Mac Figure 1 9 shows an example where a combination of Shift F1 Shift Fn F1 on Mac options BR D and BR E are used together with user defined text RNA
13. next dialog see figure 1 2 Here one can choose to include or exclude only some of the datat previously selected to work on For small numbers of data elements this would not usually be necessary However if many data objects were selected at the previous step for example to save time when choosing many data elements you could use the include or exclude functionality at this point so that only certain data elements will be be acted on by the batch rename tool The Include and Exclude filters take the text entered into the respective fields and search for matches in the names of the data elements selected in the first wizard step Thus you could enter the full names of particular data elements or just partial names Any elements where a 4 CHAPTER 1 INTRODUCTION TO BATCH RENAME 9 g Batch Rename Input 2 Filter Elements oe Fwd1 e Fwd2 xx Fwd3 x Fwd4 2c Fwd5 X Revi X Rev2 XX Rev3 XE Rev4 Filter Use comma to separate filters Exdude Indude Total input 9 Filtered 0 Remaining 9 Figure 1 2 Select how to filter the input data match is found to the term or terms in the Include field will have the batch renaming applied to them Any elements where a match is found to the term or terms in the Exclude field will not have the batch renaming applied to them For both filters if you wish to filter on more than one term at the time the individual terms must be separated wit
14. nstall To install a plugin click the Download Plugins tab This will display an overview of the plugins that are available for download and installation see figure 2 1 ea Manage Plugins Download Plugins Advanced Peak Shape Tools Plugin a Z P Provider QIAGEN Aarhus Q Support contact su io qiagen com Advanced Peak Shape Tools Version 1 0 beta 7 Build 170213 1058 156573 z Peak finding using shape information i Z eas The Advanced Peak Shape Tools Plugin provides advanced tools to manipulate peak Download and Install shapes and find regions in sequencing data that exhibit a distinct shape These tools can be used to interactively refine the results of ChIP Seq Analysis or to perform Batch Rename shape based analyses of sequencing data P Provider QIAGEN Aarhus Support contact support cicbio qiagen com The Learn Peak Shape Filter tool creates a new peak shape filter from sequencing data and a Version 1 5 Buidd 170220 1616 157004 set of positive and negative regions The Apply Peak Shape Filter tool then applies a peak shape Rename files in batch by adding a prefix or a number filter to sequencing data to discover regions peaks which match a given peak shape The Score Size 774 4 kB EREET E E Regions tool scores genomic regions according how well they match a given peak shape Bisulfite Sequencing P Provider Support contact support cicbio qiagen com Vers
15. r computer for example if you have downloaded it from our website you can install the plugin by clicking the Install from File button at the bottom of the dialog and specifying the plugin cpa file saved on your computer When you close the dialog you will be asked whether you wish to restart the workbench The plugin will not be ready for use until you have restarted 2 2 Uninstall Plugins are uninstalled using the plugin manager Help in the Menu Bar Plugins 3 or Plugins 3 in the Toolbar This will open the dialog shown in figure 2 3 The installed plugins are shown in the Manage plugins tab of the plugin manager To uninstall select Batch Rename and click Uninstall If you do not wish to completely uninstall the plugin but you do not want it to be used next time you start the Workbench click the Disable button CHAPTER 2 INSTALL AND UNINSTALL PLUGINS 13 Advanced Peak Shape Tools Plugin Beta Provider QIAGEN Aarhus Support contact support clcbio giagen com Version 1 0 beta 7 Build 170213 1058 156573 Peak finding using shape information Batch Rename Support contact support clcbio giagen com Version 1 5 Build 170220 16 16 157004 Rename files in batch by adding a prefix or a number Sequencing Bisulfite P Provider Support contact support clcbio giagen com Version 1 2 Build 170222 1036 157093 Tools to analyse bisulfite converted reads Help
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