Assuming contaminants are introduced into my sample (some of my skin sloughs off or whatever) and I use RNA-Seq to sequence my samples, if I isolated those reads via taxonomical binning, what is the likelihood they would assemble using a de novo assembler such as ABySS or Velvet?
Similarly, if reads are mis-binned into an incorrect taxonomical group via a similarity-based classifier such as MEGAN using BLASTN, what is the likelihood those isolated reads assemble?
Obviously I'm not looking for exact numbers, I'm just not aware of how likely it is to get the kind of coverage and similarity necessary for these things to assemble.
