Question: Need help to do single denovo assembly with multiple RNA seq data
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gravatar for ashokkumar.mb
5 months ago by
ashokkumar.mb0 wrote:

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

rna-seq assembly • 179 views
ADD COMMENTlink modified 5 months ago by kristoffer.vittingseerup1.7k • written 5 months ago by ashokkumar.mb0

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.

ADD REPLYlink written 5 months ago by genomax65k

Hey thank you so much, Found command for that

ADD REPLYlink written 5 months ago by ashokkumar.mb0
1
gravatar for kristoffer.vittingseerup
5 months ago by
European Union
kristoffer.vittingseerup1.7k wrote:

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.

ADD COMMENTlink written 5 months ago by kristoffer.vittingseerup1.7k
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