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How to construct Pantranscriptome from RNA_Seq data ?

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.

rna-seq pantgenomics pantranscriptomics
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updated by JC JC • written by sunnykevin97 sunnykevin97

1 answer

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.

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written by JC JC

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.

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written by sunnykevin97 sunnykevin97

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)
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written by JC JC

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