Question: de novo transcriptome assembly
gravatar for pbigbig
4.2 years ago by
United States
pbigbig200 wrote:


I have de novo RNAseq data (Illumina Hiseq) from multiple organs of a single animal. I have tried Velvet/Oases with multiples kmer against data from each organ, which finally yielded (as Oases -merge output) a transcript.fa file for each organ. Now I would like to make a whole reference transcriptome of this animal, how can I merge those transcripts obtained from multiple organs (to cut off those redundant part between them)? should I break down those transcripts.fa to kmer and reassemble them?

By the way, at the moment, which is the best suited tool for my purpose? Thank you in advance for your suggestion!


ADD COMMENTlink modified 4.2 years ago by seta1.2k • written 4.2 years ago by pbigbig200
gravatar for seta
4.2 years ago by
seta1.2k wrote:


You can use cd-hit-est tool for transcript clustering and removing redundant ones, then you may apply a tool like CAP3 to obtain the final assembly.

ADD COMMENTlink written 4.2 years ago by seta1.2k

Thank you Seta !!!

ADD REPLYlink written 4.2 years ago by pbigbig200
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