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Old 04-02-2010, 03:52 PM   #5
Location: St. Louis

Join Date: Dec 2009
Posts: 74

I will give your suggestion a try. I am not sure if the tail is poor quality or not for 100mer illumina reads, but I can use my control set to play around with the -q setting.

Its very interesting to me to hear that the max suggested -n value is 7. The fact that we are doing alignments with settings as high as -n 25 may explain some of the weird behaviors we are seeing with the aligner.

Thanks for the help.
jmartin is offline   Reply With Quote