Transdecoder

[Viraj Muthye]

Hi, I wanted to apologize for asking these very basic questions, but their answers will help me out a lot!

1. I am running transdecoder, using homology criteria PFAM. It is taking a long time to run, more than 48 hours in some instances. Is this speed normal for running Transdecoder? Is there any way I could increase the speed?

2. I am using transcriptome assemblies (Trinity) from public sources, would the changes in the header names in the Fasta files affect Transdecoder output?

Thanks!

[Brian Haas]

Hi Viraj

responses below

On Tue, May 31, 2016 at 4:07 PM, Viraj Muthye <viraj....@gmail.com> wrote:

Hi, I wanted to apologize for asking these very basic questions, but their answers will help me out a lot!

1. I am running transdecoder, using homology criteria PFAM. It is taking a long time to run, more than 48 hours in some instances. Is this speed normal for running Transdecoder? Is there any way I could increase the speed?

The TransDecoder steps themselves really shouldn't take a long while.  The latest version of TransDecoder has you run PFAM separately and provide the pfam results to the TransDecoder.predict step.  Is it the pfam step that's taking a long time, or is it TransDecoder itself?

 

2. I am using transcriptome assemblies (Trinity) from public sources, would the changes in the header names in the Fasta files affect Transdecoder output?

TransDecoder is supposed to be agnostic to the source of the transcripts and shouldn't be tied to any accession formatting.

 

Thanks!

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Brian J. Haas
The Broad Institute
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[Viraj Muthye]

Thank you for the quick response!

I believe it is the PFAM taking a long time.

[Brian Haas]

Pfam searches can be made faster by increasing the number of threads, and/or splitting up the protein database into smaller sets that can be run in parallel.

Best,

-Brian

(by iPhone)

On May 31, 2016, at 4:40 PM, Viraj Muthye <viraj....@gmail.com> wrote:

Thank you for the quick response!

I believe it is the PFAM taking a long time.

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