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454RunTimeMetricsAll.txt comprehension

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  • 454RunTimeMetricsAll.txt comprehension

    Hi,
    currently I am parsing some information from the 454RunTimeMetricsAll.txt.
    My problem is basicly to understand the layout of the file related to the actual system workflow of the 454.

    The file looks like:
    Code:
    region [1-8](
                     key(
                            sequence(...
                                    ... many accuracy values
                                    ...
                                    )
     
                            sequence(...
                                     ...
                                    )
                            )
    
                      key(...)
    
                      key(...)
    
                  )
    I need to know what are these regions, keys and sequences related to the "biology". Seems like my biology knowledge is not as good as my IT

    Thank you!

  • #2
    Regions: a 454 picotiterplate can be divided into 2, 4, 8 or 16 lanes = regions.
    key: the first four bases of each read indicate whether the read was from a sample bead, or a (spike-in) control bead (usually very few reads are control bead reads)
    sequence: for control beads only, metrics for each of the sequences in the control dataset (or for 'all' combined)

    The shortest set of metrics - usually for many more reads - are the real sample reads.

    So, not much biology... :-)

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