Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-20T18:52:21.703Z
Answers.Text: Do you think polishing with RNA-seq reads is worth it? Or is Iso-Seq alone good enough?
Answers.UserDisplayName: Caterina
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-20T20:03:04.580Z
Answers.Text: @Caterina My other answer is also applied here: polishing iso-seq data with short reads is likely to reduce the accuracy.
Answers.UserDisplayName: user172818
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-20T18:37:37.367Z
Answers.LastActivityDate: 2022-08-20T18:37:37.367Z
Answers.UserDisplayName: user172818
Body: <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>
  
Tags: <rna-seq><ngs><nanopore><pacbio>
Title: How can Iso-Seq reverse transcriptase artifacts be avoided?
ThreadText: # How can Iso-Seq reverse transcriptase artifacts be avoided?
  
  (Asked by: username_0 on 2022-08-20)
  
  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?
  
  **Tags:** rna-seq, ngs, nanopore, pacbio
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-08-20. Score: 2 | Accepted answer
  
  It is [possible to filter out](https://genome.cshlp.org/content/28/3/396) 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.
  
  > **Comments:**
  > **username_0**: Do you think polishing with RNA-seq reads is worth it? Or is Iso-Seq alone good enough?  
  > **username_1**: @username_0 My other answer is also applied here: polishing iso-seq data with short reads is likely to reduce the accuracy.  
  
  ---
  
  