How to construct Pantranscriptome from RNA_Seq data ?

Question

[sunnykevin97]

HI

I'm working in plant transcriptomics the organism I working it doesn't have any information regarding the genome and transcriptome information in public domain. Recently we sequenced RNA_seq ~20 samples from same species, my question is it possible to construct pantranscriptome from the generated denovo assemblies

Is their tools ? ,kindly suggest some suggestions as well, that I'd be great.

Answer 1

[JC]

Yes, you can reconstruct the transcriptome using de novo assembly, the best tool for this is Trinity but be sure you have a large infrastructure for this.

[sunnykevin97]

Hey, my question how to reconstruct pan-transcriptome from denovo assemblies ?, not about how to generate Denovo assembly using one pipeline.

Please, correct me If I'm wrong.

[JC]

you have 2 options:

1. pull together all libraries and assembly the mix
2. assembly each library independently and then merge all assemblies (I used CD-HIT-EST for this)

[sunnykevin97]

Thanks for the suggestion