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| SubtitleText | Add library file button on library file management page |
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| AnchorName | add-lib-file-button |
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| SubtitleText | Add library file dialog |
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| AnchorName | Add-lib-file-dialog |
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| SubtitleText | Clicking the hourglass icon displays the task progress |
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| AnchorName | lib-file-progress |
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Adding a Reference Sequence
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| SubtitleText | 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. |
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| AnchorName | add-ref-seq |
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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).
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| SubtitleText | For custom assemblies, automatic downloads are not available so the reference sequence has to be imported from another source. |
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| AnchorName | custom-ref |
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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).
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| SubtitleText | A reference sequence can be added from multiple sources |
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| AnchorName | lib-file-select-file |
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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).
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| SubtitleText | Add a reference sequence file(s) from the Partek Flow Server |
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| AnchorName | add-ref-seq-server |
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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).
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| SubtitleText | Upload a reference sequence file from your local computer through the browser |
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| AnchorName | upload-ref-seq |
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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).
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| SubtitleText | Download a reference sequence from the internet |
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| AnchorName | download-ref-seq |
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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.
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| SubtitleText | 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. |
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| AnchorName | add-cytoband |
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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).
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| SubtitleText | For custom assemblies, automatic downloads are not available so the cytoband has to be created |
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| AnchorName | custom-cytoband |
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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).
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