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Old 08-22-2009, 11:37 PM   #1
SDA
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Location: Palo Alto, CA

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Default Image re-analysis

Hi All,
We have a flow cell that we would like to re-analyze with pipeline, starting with image analysis. The reason is that this flow cell did not have a control lane, and all of the libraries had some sequence bias at the beginning, and this may have thrown off the base calling. We're planning to copy a previous run's control lane images into the image directory and then rerun the analysis, specifying the copied images as the control lane. Will this actually work? Has anyone ever tried anything like this before?
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Old 08-24-2009, 05:38 AM   #2
elaney_k
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It should work, as in the pipeline should run but I wouldn't do it that way at all ever! The control lane is used to determine metrics like phasing/prephasing etc that will vary from run to run.
I've analysed a similar run where the samples had indexes at the start and no control lane. To get around the base bias issue I ran a first pass analysis from images ignoring the indexed bases (--cycles=7-40) specifying analysis of only one lane (--tiles=s_4) and ANALYSIS none in the config file. As the sample in the lane was a genomic sample (full, not targeted) the base bias was not an issue after the index.
For the second analysis I reran the pipeline to analyse all bases and specified the matrix file from the 1st analysis (using the --matrix command) and also the phasing and prephasing using the --phasing and --prephasing command specifying the metrics obtained in the first analysis and found in the phasing.xml file in the Phasing folder.

It worked really well for me
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