Question: Denovo transcriptome assembly
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gravatar for sunil.mangalam
3.4 years ago by
United States
sunil.mangalam10 wrote:

Hi Forum,
We have some RNA-Seq data generated using Nugen's Ovation RNA-Seq System V2 kit.I plan to do denovo transcript assembly using cufflinks with this data. But when I look at the BAM files, I see many genes which have quite a lot of reads in introns. My feeling is that most of it comes from pre-mRNA (the kit uses both random primers and oligo-dT primers) although a fraction of it may be biologically meaningful (retained introns/alternate exons etc). Since cufflinks depends on junction reads for denovo assembly, having lots of premRNA will affect these types of reads and I have no idea how this will affect the results... Does anyone have any experience with denovo assembly using libraries made with this or similar kits?

Thanks!

ADD COMMENTlink written 3.4 years ago by sunil.mangalam10

My guess is that it will simply create different isoforms, with/without introns, so in some cases one of your isoforms might just be your pre-mrna and another one your mature mrna. Nothing beats trying it out.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Adrian Pelin2.2k
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