Data analysis - documentation : Pipeline calibration parameters
This page last changed on Aug 15, 2007 by maising.
The pipeline uses a number of instrument and run-specific calibration parameters. These parameters are usually auto-calibrated during a pipeline run. The meaning of the parameters is explained in more detail in the following sections. A brief description is also given in Pipeline usage.
Default offsetsA typical file "default_offsets.txt" would look like this: # Default offsets 0.00 0.00 0.00000 0.00000 -1.05 -1.62 -0.00017 0.00007 -1.20 -0.47 -0.00143 -0.00142 0.29 -0.92 -0.00159 -0.00142 It contains four lines with four values each. The first two columns in a row correspond to the values of the x- and y-offsets (in pixels) of the 4 images corresponding to A, C, G, T respectively, with respect to the A image (so the first two values are identical to zero by definition). The next two columns indicate scale factors applied to the image. A scale factor of 0 indicates that the image does not need to be rescaled. A scale factor of 0.001 for a 1000 x 1000 pixel image would indicate that images taken in the corresponding frequency channel tend to be 0.001 x 1000 = 1 pixels larger than the reference channel. Each analysis run creates a file called "Data/default_offsets.txt" in the current run-folder, which can then be used for any subsequent analysis of the same run-folder. If a file "Instruments/<instrument>/default_offsets.txt" (or in a different location if the environment variable INSTRUMENT_DIR is defined) exists, its values will be updated during the first run only. Frequency cross-talk matrixThe frequency cross-talk matrix would be specified as follows: # frequency response matrix definition > C > A > T > G 1.18 1.29 0.00 0.00 0.18 1.03 0.00 0.00 0.00 0.00 1.43 0.80 0.00 0.00 0.00 0.71 The lines starting in ">" specify the order of the rows and columns (in terms of the bases they correspond to). (If a file "Instruments/<instrument>/matrix.txt" exists, its values will be used if the "--matrix=default" option has been specified to the pipeline - see below). The frequency cross-talk matrix gets estimated during the analysis run; its estimate can be found in the file "C..._Firecrest.../Matrix/s_matrix.txt". PhasingThe phasing estimates are produced before a run of the base-caller. The file "C..._Firecrest.../Bustard.../Phasing/phasing.txt" will contain, for each tile analysed during the analysis, an estimate of the phasing and prephasing rate. The first four columns in this file indicate: lane, tile, phasing estimate, prephasing estimate. These values can be applied by the user to a subsequent run of the base-caller. As the estimation procedures uses statistical averaging over many clusters and sequences to estimate the correlation of signal between different cycles, the phasing estimates tend to be more accurate for tiles with larger numbers of clusters and a mixture of different sequences. Samples containing only a small number of different sequences do not produce reliable estimates. |
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Document generated by Confluence on Jul 25, 2008 16:42 |