pool or not to pool from different organism

Question

[sanjana]

I am planning to use Trinity for assembly. Should I pool RNA-seq data of tissues from different organism for DGE analysis?

[ATpoint]

This question is out of context, please describe your experimental setup in some detail to help people understand. A one-liner is in most cases not sufficient.

[sanjana]

I am working with data from four Bos frontalis data sets taken from 4 cows that were grown in two different altitude(two sample from one altitude). Now i am trying to do an assembly using trinity for a de novo assembly. But i am not sure if i should pool all the four data together or not.

[GenoMax]

Are the cows from the same breed/age? Were all the samples processed at the same time? If they are then you can pool the data when creating the assembly.

Is "altitude affects (or not) the gene expression" the hypothesis you are testing?

[sanjana]

Yes, I wanted to check markers associated in muscle growth of cows from different altitudes. And yes they all will be from same breed, age and will be processed in the same time. Could you please tell me whether i should pool, if yes could you please help me with the directions?