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Is there any script to select longest ORF instead longest transcript from all assembled transcripts by Trinity?

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
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updated by x.jack.min • x.jack.min • written by seta seta

2 answers

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

https://transdecoder.github.io/

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written by Damian Kao Damian Kao

Yeah, thanks.

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written by seta seta

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

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updated by Ram Ram • written by x.jack.min • x.jack.min

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