Denovo before and after an alignment

[scami]

Hi guys

I have a question to the super expert visitors of seqanswer. Ler's say I have a dataset {R} of reads and try to run an Eulerian denovo assembly on it (I am using Soapdenovo) and find 1000 contigs. I then align these reads on a reference genome. Of course I will align only those reads belonging to conserved regions between the organism I am studying and the reference one. Now, let's say I extract from the alignment file all those reads that are non aligned and can be, possibly, due to non conserved regions. I obtain a subset of the original dataset that I call {R2}. In your opinion, if I try to run a denovo assembly on R2 is there any chance I can get contigs that are different than the ones obtained upon assembly of the original dataset {R}.

thanks for your help!