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Partek Flow Documentation

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Numbered figure captions
SubtitleTextAdd a custom annotation model
AnchorNameadd-custom-annot-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). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.gtf, .gff, .gff3, .bed, .pannot, .txt and various compressed formats).

Select the source of annotation file and click Next. You must then specify the type of annotation file by choosing an option from the Annotation data type drop-down list (Figure 35). Choose mRNA for whole transcriptome annotations, where both gene and transcript level information is are present. Choose microRNA for precursor or mature microRNA transcript annotations. Choose Amplicon for targeted amplicon sequencing annotations. Choose Other for annotation files that do not fall into the other three categories (e.g. lncRNA). 

 

 

 

Numbered figure captions
SubtitleTextWhen importing an annotation model, the data type must be specified
AnchorNameimport-annot-specify-type

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For text annotations with both gene- and transcript-level information select mRNA from the drop-down  menu. You can manually specify which column corresponds to the Transcript ID or Gene ID by selecting the corresponding radio button next to the column with that information. 

 

Numbered figure captions
SubtitleTextSelect the column with gene- and transcript level information
AnchorNameannotation_model_selector

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Adding Aligner Indexes Based on an Annotation Model

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