Opened 8 years ago

Last modified 8 years ago

#593 closed task

Start filter and alignment — at Initial Version

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.16
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Part of #533.

The wizard is started after successfully demultiplexing and merging data from a sequencing run. In the first step MergedSequences items should be selected. The items need to be annotated with AnalysisResult=Successful and AutoProcessing!=Disable (eg. due to manually deselecting some libraries in the demux ended wizard).

For each selected item, the wizard create one FilteredSequences child item:

  • Name of item: <lib-name>.g.f, <lib-name>.g.f2
  • Software and protocol: (Type=Filtering)

The wizard also create one AlignedSequences grandchild item:

  • Name of item: <lib-name>.g.f.a, <lib-name>.g.f.a2
  • Software and protocol: (Type=Alignment)

Parameters for the filter step:

  • Target genome that filters away unwanted sequences. This could be hardcoded into the script, a configuration setting, or user selectable in the wizard.
  • Other parameters ????

Parameters for the alignment step:

  • Target genome to align against. This could be hardcoded into the script, a configuration setting, or user selectable in the wizard.
  • Location were the final result files should be stored. This should probably be a configuration setting.
  • Other parameters ????

After the alignment is done some information may be imported back to BASE. It would be nice to have number of aligned sequences, and possible some other information that is not yet decided.

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