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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).

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SubtitleText A reference sequence can be added from multiple sources AnchorName lib-file-select-file

 

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 AnchorName add-ref-seq-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).

 

 

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SubtitleText Upload a reference sequence file from your local computer through the browser AnchorName upload-ref-seq

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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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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SubtitleText 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. AnchorName add-aligner-index-dialog
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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:

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