<div dir="ltr">Hi, <div><br></div><div>I am in the process of doing contig assembly on a venom duct transcriptome from a marine venomous snail and have in excess of 500 million reads if I combine data fron two illumina lanes. I don't have a real way to estimate the depth of coverage required, but based on an ad hoc survey of the literature, I think this is significantly in excess of what is required for a transcriptome assembly.</div>
<div><br></div><div style>Having just read paper (Reference free algorithm etc) I have gleaned that single pass is recommended for transcriptome work in order to avoid the loss of meaningful transcripts due to an overly stringent approach. However, if I have a really significant saturation with 500 mil+ reads would a 3 pass procedure still be recommended?</div>
<div style><br></div><div style>Also I am a little concerned about "polymorphism" of my transcripts - these venom ducts are reported to produce up to 200 different toxins that exhibit variant like qualities and there may also be a fair amount of mRNA procession leading to isoforms. does this make my transcriptome an unlikely candidate for success this normalization?</div>
<div style><br></div><div style>thanks,</div><div style><br></div><div style> Liz Wright</div></div>