Is there any script to select longest ORF instead longest transcript from all assembled transcripts by Trinity?
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6.9 years ago
seta ★ 1.6k

Hi everybody,

As you all know, Trinity usually generate many transcripts. Given longest transcript is not always the best one. I'm looking for a script or tool that can select the longest ORF instead longest transcript among all generated transcripts by Trinity. Please let me know if there is such a script? Thanks

RNA-Seq Assembly sequencing sequence • 2.9k views
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6.9 years ago

TransDecoder will find best transcripts via ORF, hexamer frequency, blast, pfam:

https://transdecoder.github.io/

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Yeah, thanks.

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6.6 years ago
x.jack.min ▴ 20

http://proteomics.ysu.edu/tools/OrfPredictor.html will work for you

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