De novo assembly from DNA sequence and RNA seq

[jjjscuedu]

Hi all,

I want to ask a question about the difference between DNA sequence and RNA sequence assembly.


Do they have any difference?

For DNA sequence, which is suitable?

Because I see the popular tools for RNAseq like Trinity, ABySS, SOAP, velvet...Can they also be used to DNA sequence assembly?

Thanks!

Jingjing

[vinay052003]

The difference between DNA and RNA-Seq assembly has been reviewed very well in http://www.ncbi.nlm.nih.gov/pubmed/21897427.

For DNA assembly you can use Velvet or ABySS. ABySS was actually written for genome assembly and then was used for its extended applications for transcriptomic data.

[zgtmann]

Hi there,

May I ask you, where is difference between RNA-Seq data and sequencing form cDNA??

Thank you,

Petr.

[gringer]

Most RNA-Seq data will be from cDNA, because the sequencers are generally only designed for DNA sequencing.

In DNA assembly you have similar average coverage across the entire genome because each cell will have the same amount of DNA in it. The DNA assembly tends to be easier than RNA because there are only a few chromosomes to assemble. However, it can require a fair amount of memory because of the sheer size of each assembled chromosome, which pretty much need to be kept in memory all at once.

An RNA assembly has tens of thousands of transcripts to assemble, each with their own different relative abundance, and this abundance can change in multiple cells. RNA assembly is easier in terms of memory (because most transcripts will be 10kb or less), but more difficult due to differential splicing, differential expression, and an increased number of contigs to assemble.