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Old 08-24-2009, 05:38 AM   #2
elaney_k
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Location: Dublin, Ireland

Join Date: Mar 2008
Posts: 55
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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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