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Swift : Illumina Image Analysis/ Basecalling apratap Bioinformatics 0 10-26-2009 04:39 PM

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Old 06-06-2010, 12:41 PM   #1
Location: San Francisco, CA

Join Date: Jun 2010
Posts: 20
Default basecalling

I'm trying to recall bases on a run with goat, using parameters from another basecalling. I've tried it in 1.6.1 and 1.4.0, but in both cases, it seems to recalculate the phasing and prephasing and produce poor output. I have pasted my commands below. Can anyone see any problems in this?

/data/pipeline_in/OLB-1.6.1/bin/ 100528_6161/ --phasing=0.0028 --prephasing=0.0027 --offsets=/data/pipeline_in/Runs/100528_6161/Data/C16-36_Firecrest1.6.0_01-06-2010_root/Offsets/offsets.txt --matrix=/data/pipeline_in/Runs/100528_6161/Data/C16-36_Firecrest1.6.0_01-06-2010_root/Bustard1.6.0_01-06-2010_root/Matrix/s_3_02_matrix.txt --make

/data/pipeline_in/GAPipeline-1.4.0/bin/ 100528_6161/ --phasing=0.0028 --prephasing=0.0027 --offsets=/data/pipeline_in/Runs/100528_6161/Data/C16-36_Firecrest1.6.0_01-06-2010_root/Offsets/offsets.txt --matrix=/data/pipeline_in/Runs/100528_6161/Data/C16-36_Firecrest1.6.0_01-06-2010_root/Bustard1.6.0_01-06-2010_root/Matrix/s_3_02_matrix.txt --make
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