How to construct Pantranscriptome from RNA_Seq data ?
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5.0 years ago
sunnykevin97 ▴ 990

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 • 927 views
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5.0 years ago
JC 13k

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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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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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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Thanks for the suggestion

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