Expression analysis on Human Body Map 2.0 (HiSeq2000)

[johannes.helmuth]

Hello,

I am trying to map Human Body Map 2.0 with TopHat v1.2.0 in default settings for 50bp PE and 75 bp reads.

For 50bp PE I used a mate inner distance of 210.

After running tophat and cufflinks I can see no significant correlation between the tissues and also no correlation among same tissues in the 50bp and 75bp experiment. I assumed that there would be a > .9 correlation at least among same tissues in different experiments.

Anyone did analyze the Human Body Map data with tophat and cufflinks? Is there anything specific to notice to achieve the right results?

Thanks in advance,
Johannes