[BioC] how to find DE genes using both of 51bp data and 100bp data

[wang peter]

dear ALL
how to find DE genes using both of 51bp data and 100bp data
i have 12 samples, 6 of which are 100bp long, others are 51bp long
100bp datas cluding two conditions: treated1 treated2, treated3 vs.
 control1,control2,control3

50bp data can be seen as technical replicates of 100bp data，cluding
two conditions: treated1 treated2, treated3 vs.
 control1,control2,control3

do u know how to analyze them?  do i need classify them into 4 groups?
or 2 groups?

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shan gao
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