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Old 07-29-2014, 08:58 AM   #1
cement_head
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Red face What is the expected number of cDNAs/contigs?

Hello,

For a vertebrate, what is the expected number of cDNAs/contigs from a de novo assembly of RNA-Seq data, after the duplicates are removed?

Is there a consensus, or a rule of thumb for the minimum contig length?

Thanks,
CH
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Old 07-29-2014, 09:51 AM   #2
GenoMax
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You could use a related genome, that is reasonably finished, to make a guesstimate (http://users.rcn.com/jkimball.ma.ult...nomeSizes.html). Because of alternate splicing possibilities it would be difficult to come up with an "expected number" for cDNA.
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contig length, contig number, contig size, de novo

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