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

[Michael Campbell]

I would probably try merging the replicates but not the tissues. You can then pass the output files to MAKER in a comma separated list in the opts file.

Example: 
est=/PATH/TO/file1.fsata,/PATH/TO/file2.fasta

Good luck,
Mike

> On Jan 31, 2017, at 2:08 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> 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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