assembly cluster

[smm]

hi, i met a problem, I hava two samples,the two samples are the same species, they have a similarity of 90%,the two samples are assembled by trinity respectively, I got more than 60000,50000 unigenes respectively. i used cd-hit to remove redundancy and tgicl to cluster unigenes.i got 90000 unigenes, most unigenes are not clustered. i blast two samples, the mapped result is 75%. why most unigenes are not clustered?

[Brian Bushnell]

hi, i met a problem, I hava two samples,the two samples are the same species, they have a similarity of 90%

You have a problem already. Two samples with 90% similarity are probably different species.

Please take the time and effort to use proper spelling and grammar to clearly state what you wish to accomplish, what you have done, and what you have measured, before you post here. It is, of course, possible that you are looking at two samples of the same species, but your analysis was incorrect or your description was wrong. It's impossible to diagnose problems if you are not extremely specific. If you are talking about overlap between assembled transcriptomes, or whatever, you need to clearly state how it was calculated, and what kind of data you used. Transcriptome assembly is highly subjective and cannot trivially be used to determine whether pairs are the same species. Considering that you never used the term "RNA" anywhere in your query, it's hard to even tell what your data is or whether you are using it correctly.

[smm]

i am sorry, my english is poor, thank you for correcting me!