TransDecoder.LongOrfs AND TransDecoder.Predict

[Neo Anderson]

Dear All,

Greetings!

I have Trinity assembled plant transcripts.

I want to identify CDS.

So my question is:

Does the "TransDecoder.LongOrfs" is enough,

OR

I should go for TransDecoder.Predict also ?

Thanks in advance,

Neo

[Brian Haas]

Hi Neo,

You'll want to run through the full TransDecoder pipeline, so both steps.

best,

~b

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[Naman Mangukia]

Dear Brian,

Which one comes first ?

How can I run Full pipeline.

Please suggest me any documentation is available for pipeline.

Regards,

Neo

[Brian Haas]

Our github wiki should walk you through it:

https://github.com/TransDecoder/TransDecoder/wiki

best,

~b

[Naman Mangukia]

I have gone through the link and Ran 2 commands:

Command-1

TransDecoder.LongOrfs -t my_transcripts.fasta

Command-2

TransDecoder.Predict -t my_transcripts.fasta

Command-2 resulted in 4 files, out of which the cds file is : my_transcripts.fasta.transdecoder.cds

Did I run the correct commands ?

Regards,

Neo

[Brian Haas]

Looks like it may have worked fine

-via googleFi

[Naman Mangukia]

Thank you very much Dear Brian.

Regards, 

Neo