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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?

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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.

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  • $\begingroup$ Do you think polishing with RNA-seq reads is worth it? Or is Iso-Seq alone good enough? $\endgroup$
    – Caterina
    Commented Aug 20, 2022 at 18:52
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    $\begingroup$ @Caterina My other answer is also applied here: polishing iso-seq data with short reads is likely to reduce the accuracy. $\endgroup$
    – user172818
    Commented Aug 20, 2022 at 20:03

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