[maker-devel] Transcript assembly of RNA-seq data from different tissues and individuals

[Quanwei Zhang]

Hello:

I am trying to assemble transcripts using RNA-seq data by the tool Trinity,
which will be used for gene annotation for Maker. Now I have data from two
tissues with two replicates each. Should I merge all four samples to get
one assembly file? Or should I merge replicates of each tissue separately
and use the two assembly files as input of Maker. Merging all samples into
one, we will have much higher coverage level, but I think there may be some
genes expressed by tissue-specific isoforms. So I not sure whether I should
merge RNA-seq from different tissues.
What's more, I find some published RNA-seq data from another individual
(and also for different tissue from us) for the same species. Should I
merge all RNA-seq together (across individuals and tissues)? Or should I
generate different transcript assembly and use all those assemblies as
input to Maker?

Thanks
Best
Quanwei
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