I have a dilemma and in the current literature there are controversial opinions. The nature protocol for Trinity also is not really clear about how to treat samples derived from different tissues, although it does suggest to pool together (prior to assembly) biological and technical replicates. I would like to hear a general opinion based on experience when it comes to assemble reads from different tissues.
A) Do you pool all the reads together and then run Trinity?
B) Do you run Trinity on every distinct data set (tissue) and then merge together the outputs with another assembler (e.g. cap3)?
I think it would be interesting to know what people thinks about this and what their general results.
Thanks in advance,