Question: Transcriptome Assembly: Number Of Transcripts Expected?
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gravatar for Rm
6.2 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:

I just completed a transcriptome assembly (~ 50 Million paired end 100bps read sets) of Xenopus species without reference genome:

I followed velvet + oases multi-kmer approach with min coverage 5 and and merged the transcripts obtained from multiple Kmer (31 to 75 with step of 6) assembles: In the merged set I got around 200K Loci with around 700K total transcripts?

I was just wondering if these numbers in generally expected range? or high

velvet transcript • 1.6k views
ADD COMMENTlink modified 6.2 years ago by Istvan Albert ♦♦ 80k • written 6.2 years ago by Rm7.8k
1
gravatar for Istvan Albert
6.2 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

The number of expected transcripts is the number of existing transcripts. You can estimate that from other related genomes because even though the genomes might vary wildly the number of transcripts will probably vary a lot less.

Of course it is unlikely that any method would ever be able to match that correctly and usually you will get a lot more.

ADD COMMENTlink written 6.2 years ago by Istvan Albert ♦♦ 80k

@Istvan : Thank you; i will look over numbers from related species....

ADD REPLYlink written 6.2 years ago by Rm7.8k

i used the CD-hit-est on the merged assembly at -c 0.9 it reduced the number to ~250K

ADD REPLYlink written 6.2 years ago by Rm7.8k
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