Question: Need help to do single denovo assembly with multiple RNA seq data
0
gravatar for ashokkumar.mb
2.2 years 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 • 441 views
ADD COMMENTlink modified 2.2 years ago by kristoffer.vittingseerup3.5k • written 2.2 years 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 2.2 years ago by GenoMax94k

Hey thank you so much, Found command for that

ADD REPLYlink written 2.2 years ago by ashokkumar.mb0

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

ADD REPLYlink written 1 day ago by yahalashinnosuke0
1
gravatar for kristoffer.vittingseerup
2.2 years ago by
European Union
kristoffer.vittingseerup3.5k 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 2.2 years ago by kristoffer.vittingseerup3.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1312 users visited in the last hour