Partek Flow Documentation

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The library file management tool in Partek® Flow® provides an easy way to create, process and manage reference sequences, cytoband files, annotation models, aligner indexes, gene sets, variant databases and microarray probe sequence files.

This user guide will cover the following topics:

Library File Management settings

To review and edit library file management settings, you must be logged into Partek Flow as a user with administrator privileges. Click on the avatar in the top right corner and choose Settings. Then click System preferences on the left.

You can review the current library file directory location and privilege settings that determine whether non-administrative users can add or remove library files (Figure 1).

 

Figure 1. System preferences page showing library file directory location and privilege settings. Settings can be changed by clicking on Edit system preferences at the bottom
 

To change where the library files are stored, click Edit system preferences at the bottom and click Browse to point to another directory (Figure 2).

 

Figure 2. Changing where the library files are stored
 

You can control whether non administrative users can manage library files. If you only want administrative users to manage library files, click Edit system preferences and select the checkbox shown in Figure 3. Non Administrative users will still be able to view the library files. Unselecting the checkbox will allow any user to manage library files, but only administrative users can remove entire assemblies. The assemblies and library files created by non administrative users will be available for all Partek Flow users.

 

Figure 3. Change whether administrative or non administrative users can manage library files.

Library File Management Page

To access the library file management page click the avatar in the top right corner and choose Settings. Then click Library file management on the left.

The library file management page has two tabs - Genomic library files and Microarray library files. This section of the user guide will focus on the Genomic library files tab, which is relevant for next-generation sequencing analysis (Figure 4).

 

 

Figure 4. Genomic library files page
The gray arrows (/) expand/collapse each section. Associated library files are shown in a table in each section. The view file () icon in the Actions column of each table displays additional library file details. The red cross () dissociates a library file. The hourglass () icon indicates a library file is being created

Selecting an Assembly

Choosing an Assembly from the drop-down list at the top will display the associated library files in the pane below. Assemblies are named by the species and the build version (e.g. Homo sapiens (human) - hg19). Different build versions for the same species are regarded as separate assemblies (Figure 5). Administrative users can delete a selected assembly by clicking the red cross ().

 

 

Figure 5. Human assembly versions hg17, hg18 and hg19 will appear as separate assemblies in the drop-down list.

Library Files

The library files associated with the selected assembly are organized into six major sections (Figure 4, above).

Below is some information on each section. For more detail on adding library files, see the Adding library files to an assembly on the library file management page section of this user guide.

Reference Files. This section includes two types of library file: reference sequence and cytoband files.

Reference sequences are the chromosome/scaffold/contig DNA sequences for a species. A reference sequence file is typically in FASTA or 2bit format. The reference sequence of a species is used for aligner index creation, variant detection against the reference sequence and visualization of the reference sequence in the Chromosome view.

Cytoband files are used for drawing ideograms of chromosomes in the Chromosome view, including positions of cytogenetic bands if known.

Reference aligner indexes. Next-generation sequencing aligners require the reference sequence to be indexed prior to alignment, as this greatly increases alignment speed. An index consists of a set of files (Figure 6) and are generally aligner specific. For example, if you wish to align using BWA, you need a BWA index.

 

 

Figure 6. BWA reference aligner index files for human hg18 assembly
Some of the supported aligners share indexes. If you want to align using Tophat, the Bowtie aligner indexes can be used. If you want to align using Tophat2, the Bowtie2 aligner indexes can be used.

Some aligner indexes are version specific, so care must be taken if you change aligner versions. For example, the index files for STAR version 2.4.1d are different to older versions of STAR.

This section contains aligner indexes for aligning to the whole genome. If you wish to align to a subset of the genome, e.g. targeted amplicons or the transcriptome, you must generate these indexes in the Annotation models section.

Gene sets. Gene set files are required for biological interpretation analyses (e.g. GO enrichment). Genes are grouped together according to their biological function. Gene set files have to be in GMT format, where each row represents one gene set. The first column of a GMT file is the GO ID or gene set name. The second column is an optional text description. Subsequent columns are the gene symbols that belong to each gene set. Gene ontologies for various model organisms are available for automatic download from the Partek repository (source: geneontology.org). Because gene ontologies are frequently updated, geneontology.org is checked for updates quarterly. You can check for recent updates to the Partek repository on the Partek website.

Variant annotations. Variant annotation databases are collections of known genomic variants (e.g. single nucleotide polymorphisms). If you have performed a variant detection study, detected variants can be searched against variant annotation library files to see if the detected variants are known from previous studies. Furthermore, you can validate detected variants against 'gold-standard' variant annotation library files. Variant annotation files are typically in VCF format.

Variant annotation databases from commonly used sources (e.g. dbSNP) are available for automatic download from the Partek repository. Because variant annotation databases are frequently updated, these sources are checked for updates quarterly. You can check for recent updates to the Partek repository on the Partek website.

SnpEff variant databases. SnpEff (1) is a variant annotation and effect prediction tool that requires its own variant annotation files, separate to the other Variant annotation library files. If you wish to use SnpEff, library files need to be added to this section.

Annotation models. This section includes two types of library file: annotation models & aligner indexes.

Annotation models describe genomic features (e.g. genes, transcripts, microRNAs) for a specific version of the reference sequence. Annotation models contain labels (e.g. gene ID) and genomic coordinates (e.g. chromosome, start & stop position) for each feature.

Annotation models will appear in separate tables (Figure 7). If you have multiple versions of annotation models from the same source, it is advisable to distinguish them by their date or version number.
Annotation models from commonly used sources (e.g. Refseq, ENSEMBL) are available for automatic download from the Partek repository. Because annotation models are frequently updated, these sources are checked for updates quarterly. You can check for recent updates to the Partek repository on the Partek website.

Annotation models are used for quantification in gene expression analyses, annotating detected variants (e.g. to predict amino acid changes), visualizations in Chromosome view, generating coverage reports and for aligner index creation (see below). Typical file formats include GTF, GFF, GFF3 and BED.

 

 

Figure 7. Annotation models are displayed in separate tables.
The gray arrows (/) next to the annotation model name expand/collapse each table. The three annotation models displayed in Figure 7 are different versions from the same source (RefSeq), distinguishable by their date. Aligner indexes (e.g. for alignment to the transcriptome) are added to the table of the corresponding annotation model.

The aligner indexes in the Annotation models section are required if you wish to align to a subset of the genome as defined by the annotation model, e.g. target amplicons or the transcriptome. The reference sequence is still required to generate an aligner index for an annotation model. As with whole genome alignment, indexes are aligner specific, although some aligners share indexes and are version specific (see Reference aligner indexes above). The aligner indexes generated will be added to the corresponding annotation model table (Figure 7, above).

Update Library Index

The library index is a file that contains download sources for all Partek distributed library files. An automatic update of this file will occur every 24 hours (Figure 8), so this normally doesn't require any attention. If you do wish to manually update the library index, click Update Library Index at the bottom of the library file management page.

 

 

Figure 8. The date and time the library index was last updated is displayed at the bottom of the library file management page.

Creating an Assembly on the Library File Management Page

On the library file management page, an assembly can be added by choosing Add assembly… from the Assembly drop-down list (Figure 9). If the list is long, you may need to scroll to the bottom.

 

 

Figure 9. Adding an assembly on the library file management page
In the Add assembly dialog, choose the Species from the drop-down list (Figure 10), followed by the Assembly version (Figure 11) and click Add. The dialog will automatically load commonly used assembly versions for the selected species (Figure 11). If the assembly version you want does not appear in the list, choose Other and type the custom assembly version name (Figure 12). Note that If an assembly version for a given species already exists on your system, it will not appear in the drop down list.

 

 

Figure 10. Add assembly dialog. The species can be chosen from the drop-down list

 

 

Figure 11. For the chosen species, commonly used assembly versions can be chosen from the drop-down list

 

 

Figure 12. A new assembly version can be added by choosing Other and typing the custom assembly version name manually

If the species you want to add does not appear in the list, scroll to the bottom of the species list, choose Other and manually type the species name and assembly version (Figure 13).

 

 

Figure 13. A new species can be added by typing the name and assembly name manually

Adding Library Files on the Library File Management Page

Library files can be added to an assembly by clicking the green plus (  ) icon next to the header of each section (Figure 14) on the library file management page. This will open a dialog specific to the chosen section. If all possible library files are already associated in each section, the green plus icon will appear gray (Figure 14).

 

 

Figure 14. The green plus icon is used to add library files to a section on the library file management page (left). The icon turns gray if all possible library files have been added to a section (right).
Alternatively, library files can be added by clicking on the green Add library file button on the library file management page (Figure 15). Choose a library type from the drop-down list in the Add library file dialog (Figure 16) and the dialog will present options specific for each type. If certain library files have already been associated with an assembly, they will not appear as options in the dialogs. For example, if a reference sequence has already been associated with an assembly, it will not appear as an option in the drop-down list shown in Figure 16.

 

 

Figure 15. Add library file button on library file management page

Figure 16. Add library file dialog

All library file tasks are logged in the System queue, which can be accessed by clicking on the avatar in the top right corner, choosing Settings and clicking System queue on the left. When a library file is being created, the hourglass icon (  ) will appear in the Actions column (Figure 4, above). Clicking this icon will display information on the task progress (Figure 17).

 

 

Figure 17. Clicking the hourglass icon displays the task progress

Adding a Reference Sequence

Click the green plus (  ) icon next to the Reference Files section header (Figure 14, above) and choose Reference sequence from the Library type drop-down list in the Add reference sequence dialog (Figure 18). Alternatively, click the Add library file button and choose Reference sequence from the Library type drop-down list (Figure 16, above). If a cytoband file is already associated with an assembly, Reference sequence will be the only option available in the Add reference sequence dialog and will not appear in a drop-down list (Figure 18).

 

 

Figure 18. Add reference sequence dialog. If the reference sequence and cytoband files have not been added yet, both options will appear in the Library type drop-down list (left). If one is missing, it will appear as the only option (right). For many model organisms, automatic downloads are available from the Partek repository.
If you are using an assembly supported by Partek (e.g. human), there are two radio button options: Download reference sequence and Import reference sequence (Figure 18, above). Select Download reference sequence and click Create to get the reference sequence from the Partek repository. Alternatively, select Import reference sequence and click Create to add the reference sequence from another source.
If you are using a custom assembly (e.g. for a non-model organism), only the Import reference sequence radio button will be available (Figure 19).

 

 

Figure 19. For custom assemblies, automatic downloads are not available so the reference sequence has to be imported from another source.
The Import reference sequence option allows you to add a reference sequence from the Partek Flow Server, My Computer or a URL download link (Figure 20).

 

 

Figure 20. A reference sequence can be added from multiple sources
To add a reference sequence from the Partek Flow server, select Partek Flow Server, click Browse and navigate to the directory storing the reference sequence file(s) (Figure 21). Only files with the correct file extensions (.fa, .2bit or any compressed format) will be displayed in the file browser. Select the checkbox next to the file name(s) you wish to import and click Continue (Figure 21). Click Finish to add the selected reference sequence file(s) (Figure 20).

 

 

Figure 21. Add a reference sequence file(s) from the Partek Flow Server
To upload a reference sequence from your local computer select My computer, click Choose file and navigate to the location of the file(s) on your local machine (Figure 22). It is not advisable to upload large files through the web browser, as this will likely result in an error (e.g. an upload timeout). Administrative users are able to set a limit on the upload file size via System preferences (Figure 1, above). The default file size limit is 500 MB. Please note that only one file can be uploaded at a time. Click Finish to add the selected reference sequence file(s) (Figure 22).

 

 

Figure 22. Upload a reference sequence file from your local computer through the browser
To download a reference sequence (e.g. from a public repository such as ENSEMBL), select URL and input the URL address (Figure 23). Make sure to include the full URL address, starting with the transfer protocol (e.g. http:// or ftp://) and ending with the file name. It is advisable to find the download link address, copy it to the clipboard and paste it into the Input URL box. Click Finish to add the selected reference sequence file(s) (Figure 23).

 

 

Figure 23. Download a reference sequence from the internet
Note that you can specify multiple fasta files (e.g. one file per chromosome) and Partek Flow will concatenate them. If a fasta file is imported, a 2bit version of the file will automatically be created, and visa-versa. Partek Flow will also accept a range of compressed file formats (gzip, bzip2, zip, tar). If a compressed file is imported, it will automatically be uncompressed and processed.

Adding a Cytoband

Click the green plus (  ) icon next to the Reference Files section header (Figure 14, above) and choose Cytoband from the Library type drop-down list in the Add reference sequence dialog (Figure 24). Alternatively, click the Add library file button and choose Cytoband from the Library type drop-down list (Figure 16, above). If a reference sequence is already associated with an assembly, Cytoband will be the only option available in the Add genome dialog and will not appear in a drop-down list (Figure 24).

 

 

Figure 24. Add reference sequence dialog. If the reference sequence and cytoband files have not been added yet, both options will appear in the Library type drop-down list (left). If one is missing, it will appear as the only option (right). For many model organisms, automatic downloads are available from the Partek repository.
If you are using an assembly supported by Partek (e.g. human), there are two radio button options: Download cytoband and Create cytoband from 2bit (Figure 24). Select Download cytoband and click Create to get the cytoband file from the Partek repository. Alternatively, select Create cytoband from 2bit and click Create to build the cytoband file. If the reference sequence is missing, it will either be downloaded automatically or you will be asked to import it from another source (see Adding a reference sequence).

If you are using a custom assembly (e.g. for a non-model organism), only the Create cytoband from 2bit option is available (Figure 25).

 

 

Figure 25. For custom assemblies, automatic downloads are not available so the cytoband has to be created

Adding Reference Aligner Indexes

Note that this task is for adding indexes for alignment to the whole genome. If you want to align to the transcriptome or another set of genomic features, see Adding Aligner Indexes Based on an Annotation Model below.

Click the green plus (  ) icon next to the Reference aligner indexes section header. Alternatively, click the Add library file button, choose Aligner index from the Library type drop-down list (Figure 16, above) and whole genome from the Index to drop-down list. If an aligner index is already associated with an assembly, it will not appear in the Aligner drop-down list. If all but one of the possible aligner indexes have been added, the remaining aligner index will be the only option and will not appear in a drop-down list (Figure 26).

 

 

Figure 26. Add aligner index dialog. If more than one aligner index has not been added to an assembly, the missing aligner indexes will appear in the drop-down list (left). If only one aligner index remains to be added, it will be the only option (right). For many model organisms, automatic downloads are available from the Partek repository.
Choose the aligner index you wish to add from the drop-down list in the Add aligner index dialog (Figure 27). The following indexes can be added:

  • Bowtie
  • Bowtie colorspace
  • Bowtie 2
  • TMAP
  • BWA
  • SHRiMP 2
  • SHRiMP 2 colorspace
  • Issac 2
  • STAR
  • STAR 2.4 1d
  • GSNAP
  • GSNAP v8


If you are using an assembly supported by Partek (e.g. human), there are three radio button options: Download index; Build index or Import index (Figure 26). Certain aligner indexes may not be available for automatic download because the file sizes are too large to download efficiently.

If available, select Download index and click Create to get the chosen reference aligner index from the Partek repository.

Alternatively, select Build index and click Create to build the reference aligner index. To build an aligner index, a reference sequence file must already be associated with the assembly. Depending on the aligner, you may have to specify further parameters. Consult the user documentation for each aligner for guidance (usually available on-line).

Alternatively, select Import index and click Create to add an aligner index from another source. An aligner index can be added from the Partek Flow Server, My Computer or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a reference sequence, above). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible. This will vary for each aligner.

For custom assemblies (e.g. for non-model organisms), only the Build index and Import index options are available (Figure 27).

 

 

Figure 27. For custom assemblies, automatic downloads are not available so the aligner indexes has to be built or imported

Adding a Gene Set

Click the green plus (  ) icon next to the Gene sets section header. Alternatively, click the Add library file button and choose Gene set from the Library type drop-down list (Figure 16, above).
If you are using an assembly supported by Partek (e.g. human), a gene set from geneontology.org will appear in the Add gene set drop-down list (Figure 28). Select the Download gene set radio button and click Create.

 

 

Figure 28. For many model organisms, automatic downloads of gene sets are available from the Partek repository (source: http://geneontology.org/)
If you prefer to add a custom gene set, or if you are working with a custom assembly, choose Add gene ontology source from the Add gene set drop-down list (Figure 29). Name the gene set by typing into the Custom Name box and click Create. A gene set file can be added from the Partek Flow Server, My Computer or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a reference sequence, above). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.gmt and various compressed formats).

 

 

Figure 29. Adding a custom gene set

Adding a Variant Annotation Database

Click the green plus (  ) icon next to the Variant annotations section header. Alternatively, click the Add library file button and choose Variant annotations from the Library type drop-down list (Figure 16, above)
If you are using a human - hg19 assembly, variant annotation databases from various sources will appear in the Variant annotation drop-down list (Figure 30). Available variant annotation database sources include:

  • dbSNP
  • Kaviar
  • NHLBI Variant Server
  • 1000 Genomes

Multiple versions of the above databases are available. For human - hg38, only dbSNP is currently available. This list is periodically updated.

 

 

Figure 30. For human - hg19, automatic downloads of various variant annotation databases are available from the Partek repository.
Choose a database from the drop-down list, select the Download variant database radio button and click Create.

If you prefer to add a custom variant annotation database, perhaps from another source or 'gold-standard' validated variants, choose Add variant database from the Variant annotation drop-down list (Figure 31). Name the variant annotation database by typing into the Custom Name box and click Create. A variant annotation database can be added from the Partek Flow Server, My Computer or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a reference sequence, above). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.vcf and various compressed formats).

 

 

Figure 31. Add a custom variant annotation database

Adding a SNPEff Variant Database

Click the green plus (  ) icon next to the SNPEff variant databases section header. Alternatively, click the Add library file button and choose SNPEff variant database from the Library type drop-down list (Figure 16, above).

If you are using human (hg19 and hg38), mouse (mm10) or rat (rn5 and rn6) assemblies, various versions of SNPEff variant databases are available for automatic download (Figure 32).

 

 

Figure 32. Various versions of SNPEff variant databases are available for automatic download. The drop-down list shows databases available for human - hg19 Choose a SNPEff database from the drop-down list, select the Download SNPEff variant database radio button and click Create.

Adding an Annotation Model

Click the green plus (  ) icon next to the Annotation models section header and choose Gene/feature annotation from the Library type drop-down list in the dialog (Figure 33). Alternatively, click the Add library file button and choose Gene/feature annotation from the Library type drop-down list (Figure 16, above).

If you are using an assembly supported by Partek (e.g. human), annotation models from a variety of commonly used sources (e.g. RefSeq, ENSEMBL, GENCODE) will appear in the Annotation model drop-down list in the dialog. Choose an annotation model, select the Download annotation file radio button and click Create (Figure 33).

 

 

Figure 33. For many model organisms, automatic downloads of gene/feature annotation models from various sources are available from the Partek repository.
If you prefer to add a custom annotation file or if you are working with a custom assembly, choose Add annotation model from the Annotation model drop-down list (Figure 34). You may need to scroll to the bottom of the drop-down list to see this option. Name the annotation model by typing into the Custom Name box and click Create.

 

 

Figure 34. Add a custom annotation model
A custom annotation model can be added from the Partek Flow Server, My Computer or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a reference sequence, above). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.gtf, .gff, .gff3, .bed, .pannot and various compressed formats). You must specify the type of annotation file by choosing an option from the Annotation data type drop-down list (Figure 35).

 

 

Figure 35. When importing an annotation model, the data type must be specified

Adding Aligner Indexes Based on an Annotation Model

Note that this task is for adding indexes for alignment to a subset of the genome (e.g. the transcriptome). If you want to align to the whole genome, see Adding Reference Aligner Indexes above.

Click the green plus (  ) icon next to the Annotation models section header and choose Aligner index from the Library type drop-down list in the dialog (Figure 36). Alternatively, click the Add library file button, choose Aligner index from the Library type drop-down list (Figure 16, above).

Choose the aligner you wish to use from the Aligners drop-down list (Figure 36). All 10 aligners are available for indexing to an annotation model.

The annotation model(s) that have already been associated with an assembly will appear at the top of the Index to drop-down list. Choose the annotation model you wish to index to, select the Build index radio button and click Create (Figure 36). To build an aligner index based on an annotation model, a reference sequence file must already be associated with the assembly.

If you are using an assembly supported by Partek (e.g. human), annotation models from a variety of commonly used sources will appear in the Index to drop-down list in addition to the ones that have already been associated with the assembly. If you choose an annotation model that has not already been associated, it will automatically be downloaded prior to building the index.

 

 

Figure 36. Building an aligner index for an annotation model

Adding Library Files from Within a Project

Missing library files can be added when setting up tasks within a project, without having to navigate to the library file management page. The user interface will vary depending on the task and which library files already exist on your system. Below are two examples scenarios.

Adding a missing whole genome aligner index (Bowtie 2 in this example)

  1. Under the Analyses tab of a project, select an Unaligned reads data node
  2. From the toolbox on the right, choose Aligners followed by Bowtie 2

On the alignment task setup page, Partek Flow will display all assemblies that have a Bowtie 2 index (whole genome and transcriptome) in the Assembly drop-down list. If the assembly you want is missing, choose New assembly… from the drop-down list (Figure 37)


Figure 37. The drop-down list will show all assemblies that have a Bowtie 2 index associated with them. Choose New assembly... to add a Bowtie 2 index to another assembly.
 

  1. Choose the species and assembly in the Add Bowtie 2 index dialog. If the species and assembly you want do not appear in the drop-down lists, choose Other and manually type the names (Figure 38)
  2. Choose Whole genome from the Index drop-down list (Figure 38)
  3. Select the Build index radio button (Figure 38)
  4. Click Create (Figure 38)

 

 

Figure 38. Add Bowtie 2 index to another assembly not listed in Figure 38.
Once the new Bowtie 2 index has been specified, you are able to queue the alignment task and it will execute once the Bowtie 2 index has been built.

Add a missing gene set file for enrichment analysis

  1. Under the Analyses tab of a project, select a Feature list data node
  2. Choose Biological interpretation from the menu on the right, followed by Enrichment analysis
  3. If there are no gene set files associated with the relevant assembly, click Create gene set (Figure 39)


    Figure 39. If no gene sets are associated with the assembly, click the button to add one.

  4. If you are working with an assembly/species supported by Partek (e.g. human), choose a gene set from the Create gene set drop-down list (Figure 40), select the Download gene set radio button and select Create. Alternatively, choose Add gene ontology source from the Create gene set drop-down list, manually type the custom gene set name and click Create to import your own gene set from the Partek Flow server, My computer or URL (Figure 41). If you are working with a custom species/assembly (e.g. for a non-model organism), only the Add gene ontology source option is available.



Figure 40. Download a gene set using the Create gene set dialog from within a project
Figure 41. Import a gene set using the Create gene set dialog from within a project

Microarray Library Files

Microarray library files can be managed by clicking the Microarray libraries tab on the Library file management page (Figure 42). The chip name and download source of stored Microarray library files are shown in the table.

 

 

Figure 42. Microarray libraries files tab
Microarray probe tab files are used for processing microarray data in Partek Flow. When microarray intensity data files (e.g. Affymetrix .CEL files) are imported into a project, the chip type is automatically detected and the appropriate probe tab annotation file is downloaded. Thus, you would normally not need to manually add any probe tab annotation files.

To manually download a probe tab file, click the green Add probe sequence button at the top of the page (Figure 42, above). Choose the chip name from the drop-down list in the dialog, select the Download probe sequence radio button and click Create (Figure 43). If a chip has already been added, it will not appear in the Chip name drop-down list. We currently support automatic downloads of a broad variety of Affymetrix and Illumina microarray chips.

 

 

Figure 43. Manually download microarray probe tab annotation files
To add a custom probe tab file (e.g. for a custom chip), click the green Add probe sequence button at the top of the page (Figure 42, above). Scroll to the bottom of the Chip name drop-down list and choose Other / Custom. Name the chip by typing into the Custom Name box and click the Create button (Figure 44).

 

 

Figure 44. Adding a custom probe tab file e.g. for a custom microarray chip
A custom probe tab file can be added from the Partek Flow Server, My Computer or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a reference sequence, above). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.probe_tab and various compressed formats). Please see the Importing Custom CEL files user guide for more information.

References

  1. Cingolani P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 6(2):80-92. PMID: 22728672

 

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