Introns

[selmanurk]

Hi everyone,
I am trying to analyze some transcriptome assembly I created via Trinity. Considering the final nucleotide sequence is called .cds, does transcdecoder exclude introns? Because I am looking for intron retention I wouldn't want that. Thank you,
S

[brianjohnhaas]

Hi, TransDecoder isn't aware of the presence or absence of introns in the Trinity reconstructed transcripts. If you have intron retention, though, it'll often result in early coding termination, unless it's full read-thru the intron sequence. With plants and fungal transcriptomes, introns tend to be short and you could get a fully retained intron assembled. For long introns (several kb or more), it's less likely to assemble as a retained intron based on my experience.

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On Sat, Aug 6, 2022 at 11:29 AM selmanurk ***@***.***> wrote: Hi everyone, I am trying to analyze some transcriptome assembly I created via Trinity. Considering the final nucleotide sequence is called .cds, does transcdecoder exclude introns? Because I am looking for intron retention I wouldn't want that. Thank you, S — Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXYKKOIJVG2F3KBOYKTVX2AGDANCNFSM55YY2MMQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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