Question: Is there any script to select longest ORF instead longest transcript from all assembled transcripts by Trinity?
1
gravatar for seta
4.3 years ago by
seta1.2k
Sweden
seta1.2k wrote:

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

ADD COMMENTlink modified 4.0 years ago by x.jack.min20 • written 4.3 years ago by seta1.2k
1
gravatar for Damian Kao
4.3 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

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

https://transdecoder.github.io/

ADD COMMENTlink written 4.3 years ago by Damian Kao15k

Yeah, thanks.

ADD REPLYlink written 4.3 years ago by seta1.2k
0
gravatar for x.jack.min
4.0 years ago by
x.jack.min20
x.jack.min20 wrote:

http://proteomics.ysu.edu/tools/OrfPredictor.html

will work for you

 

 

 

ADD COMMENTlink written 4.0 years ago by x.jack.min20
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