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**TransDecoder for Transcriptome Data**
 
Documentation by Kate Glennon, Sarah Shah, and Shelby Williams.
 
The TransDecoder is used to get the amino acids from a transcriptome. It will predict the coding regions.
 
1. To run, you will need to make a copy of your transcriptome fasta file in a new folder. Use the command line:
  * /opt/perun/TransDecoder-3.0.1/TransDecoder.LongOrfs -t YourTranscriptome.fasta
2. Once this has finished, you will run the TransDecoder Prediction to get the final coding region predictions. Use the following command line, with the same transcriptome file:
  * /opt/perun/TransDecoder-3.0.1/Transdecoder.Predict -t YourTranscriptome.fasta

This will result in your final predictions, and the output files that you want to use are the transcoder.pep files. 

You can rename the headers or remove certain characters you do not want (such as *) by:
  * awk '/^>/{print ">" ++i; next}{print}' < inputfile > outputfile        #This renames the headers to >numbers
  * sed 's/*/ /g' inputfilename > outputfilename         #This removes the asterisk characters.