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cansyl / ECPred

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Runing of ECPred on plants data ? #4

Closed anani-a-missinou closed 2 years ago

anani-a-missinou commented 4 years ago

Hi,

Can I apply your tools on plant data that contained many genes from polyploidization and tandem duplication? So potentially neofunctionalization or sub-functionalization of genes. Thanks

alperendalkiran commented 4 years ago

Yes, you may use ECPred on your data. We used the tool on metagenomics sequencing data for genome annotations. Metagenome data is in a way similar to your data. Don’t forget to translate your plant ORF data in amino acid sequences, since ECpred works with protein sequences, good luck.

anani-a-missinou commented 4 years ago

Thank you for your answer.

I try to install ECPred on Virtual Ubuntu 18 machine install on Cluster. by this following script

sudo apt-get install default-jre sudo apt-get install default-jdk

wget https://ucfa50bebca5bb3d75722c012574.dl.dropboxusercontent.com/cd/0/get/AwGEe7EWD7EQ48aCNJg-DSPK_oTK7PFFjjmZw7bvzA303TOAl1tEs1OnPBCc6vP0oH1bu5S95Fs13-DOCtX5DWXObc2pZiSx5Ju4sHrM_78CMA/file?dl=1# wget https://goo.gl/g2tMJ4

This file download return this file ‘file?dl=1’ which is not zipped. I think it incorrectly downloads of ECPred.tar.gz file which normally contained all required files including ECPred.jar when I download on my windows system.

ECPred\lib ECPred\ECPred.jar ECPred\ECPred_woH.jar ECPred\ECNumberList.txt ECPred\README ECPred\README_woH ECPred\results.tsv ECPred\runLinux.sh ECPred\runMac.sh ECPred\sample.fasta

Please, can you help me with the correct installation and use it.

alperendalkiran commented 4 years ago

Could you please re-download using the following command, wget -O ECPred.tar.gz https://goo.gl/g2tMJ4