Need help to do single denovo assembly with multiple RNA seq data

Question

[ashokkumar.mb]

I have illumina RNA seq data from different tissues of one plant. Is it possible to do single assembly using all this RNA seq data from different tissues of one plant? Do I need to combine this libraries before assembly or is there any option in assembly tools itself?

Thank you

[GenoMax]

Yes. Take a look at Trinity.

Depending on the amount of your data RAM requirements can be high but it is a well accepted option for eukaryotic transctiptome assembly.

[ashokkumar.mb]

Hey thank you so much, Found command for that

[yahalashinnosuke]

May I ask which command is that? I have the same question , need to combine different tissue RNAseq data of one plant. Thank you!

Answer 1

[Kristoffer Vitting-Seerup]

If you have a refrence genome tools such as Cufflinks or StringTie will work better - I have a small section in my vignette describing this here.