Question: De novo assembly average length
0
gravatar for aatif1903
4.5 years ago by
aatif19030
aatif19030 wrote:

Hello everyone. I have did de novo assembly by using CLC Bio. I have an average length of transcripts about 119bp. Is this length enough for correct annotation?

rna-seq assembly • 1.6k views
ADD COMMENTlink modified 4.5 years ago by Brian Bushnell17k • written 4.5 years ago by aatif19030

Average is a bad statistic (of most things). Try to plot the distribution, maybe the average get's dragged down by unassembled short fragments.

On average, a human has slightly less than one testicle. I think that we can agree that that is not representative of the true distribution. On average, there are two popes per square kilometer in the Vatican.

ADD REPLYlink written 4.5 years ago by WouterDeCoster45k
1
gravatar for Brian Bushnell
4.5 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

Average length is not a useful statistic in assembly. L50 (the length of the at which 50% of the assembled bases are in contigs of at least that length) is much more useful.

Generally, 119 bp contigs are useless for annotation; and where your contigs are shorter than your reads, assembly failed.

ADD COMMENTlink written 4.5 years ago by Brian Bushnell17k
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