text: user14030: My end goal is annotate a de-novo assembled genome. When trying to select the best method for transcriptome assembly I read Iso-seq was the preferred method. However other people suggested Nanopore as reverse transcriptase artifacts can be avoided. Is there any other way one can avoid these artifacts without the need for Nanopore?
  Also, what is the recommended depth? Is using more SMRTcells worth the cost?
  
  user37: It is possible to filter out iso-seq reads with RT artifacts, though I don't know how effective these informatics approaches are. With nanopore, you will get more false junctions in alignment or transcript assembly due to sequencing errors. I more often see iso-seq used for new species.
  
original_text: 14030: <p>My end goal is annotate a de-novo assembled genome. When trying to select the best method for transcriptome assembly I read Iso-seq was the preferred method. However other people suggested Nanopore as reverse transcriptase artifacts can be avoided. Is there any other way one can avoid these artifacts without the need for Nanopore?
  Also, what is the recommended depth? Is using more SMRTcells worth the cost?</p>
   37: <p>It is <a href="https://genome.cshlp.org/content/28/3/396" rel="nofollow noreferrer">possible to filter out</a> iso-seq reads with RT artifacts, though I don't know how effective these informatics approaches are. With nanopore, you will get more false junctions in alignment or transcript assembly due to sequencing errors. I more often see iso-seq used for new species.</p>
  