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Old 04-02-2014, 02:19 AM   #1
variadevang
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Question Using CEGMA

Hello Guys,
I have a project task, and i need to implement CEGMA for validating the predicted genes in the de-novo assembly. i have successfully installed and done a test run for CEGMA. and it produces a correct output for the sample data.
Apart from that i have no idea on what are the inputs for cegma, do we have to download the datasets which are mentioned on the website (http://korflab.ucdavis.edu/datasets/cegma/#SCT6) under the section of Core eukaryotic genes dataset.
Would really appreciate if someone can explain in simple words, about how to use cegma!
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Old 04-02-2014, 07:18 AM   #2
kbradnam
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The input is a single FASTA file of the genome (or even transcriptome) assembly that you are trying to assess.

The FASTA file must have unique identifiers and not contain characters in the definition line which break NCBI's makeblastdb command.
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Old 04-02-2014, 07:20 AM   #3
kbradnam
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P.S. If your species is not a mammalian or vertebrate species (which have longer introns that CEGMA has command-line options for), you can just run it very simply:

cegma -g your_genome_assembly.fasta -T <n>

Where <n> is the number of threads your computer is able to utilize. This can be used to speed things up.
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Old 04-03-2014, 01:27 AM   #4
variadevang
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Smile Thank You!

thanks a lot kbradnam. Appreciate the help!
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