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Old 02-02-2012, 11:13 AM   #1
aggp11
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Default CASAVA 1.8 --use-bases-mask

Hi,

I am trying to learn how to use CASAVA 1.8. I am trying to demultiplex the samples using the configureBclToFastq.pl . I am having trouble understanding the --use-bases-mask option. For example, if I have a 2X75 bp PE run with 6bp long indices, then would the following be correct:

--use-bases-mask y75n,I6n,Y75n

Could anybody please help me understand it?

Thanks,
P
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Old 02-02-2012, 11:22 AM   #2
amitm
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hi aggp11,
Yes that is correct. In case you want to call all the sequenced bases (read+index), then specifying --use-bases-mask is not needed as Casava would detect it from the XML config files. Say you want to read only the first 70bases of each read, then the option would be written as -
--use-bases mask y70nnnnnn,I6n,y70nnnnnn

The n's from the last specify the bases to be not called. For 75bp seq., Illumina runs 76cycles. The last base being of low quality, generally, can be left out by saying 75n. Similarly, for the index also, 7 cycles are run where the last is left out by default.
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Old 02-02-2012, 12:13 PM   #3
sklages
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Quote:
--use-bases mask y70nnnnnn,I6n,y70nnnnnn
short: --use-bases mask y70n6,I6n,y70n6
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Old 02-02-2012, 12:28 PM   #4
amitm
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thanks :-)
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Old 02-02-2012, 05:34 PM   #5
RCJK
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I was just trying to do this yesterday, thanks for clarifying it!!
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