Hi there,
I got a couple of question for you today. If I want to get the information
about the Biological Abundance and the GeneOntology Terms in the same
analysis, how should I proceed? If I'm putting two search terms in the
command line, would it be alright and detect automatically where to look
for each analysis step?
Ex :
mpiexec -n 48 Ray -k 31 -p Sample.filtered.R1.fq.gz
Sample.filtered.R2.fq.gz -s Sample.filtered.single.fq.gz -o RAY_k31_c100
-search ~/NCBI-taxonomy/NCBI-Finished-Bacterial-Genomes -with-taxonomy
~/NCBI-taxonomy/Genome-to-Taxon.tsv ~/NCBI-taxonomy/TreeOfLife-Edges.tsv
~/NCBI-taxonomy/Taxon-Names.tsv -search ~/GeneOntology/EMBL_CDS_Sequences
-gene-ontology ~/GeneOntology/OntologyTerms.txt
~/GeneOntology/Annotations.txt
Another question, I tried to redo the same files as on your 2012 Paper (as
found on GitHub) using all your scripts you provide there:
https://github.com/sebhtml/Paper-Replication-2012/tree/master/Build-Input-Files-for-Gene-Ontology
And I'm not able to get this completed. The script Rebuild-Fasta.py
apparently does nothing at the end of the day. It's creating
EMBL_CDS_Sequences folder, but the only file in it is empty and the rest of
the procedure is not producing the right things.
Can you help me with this or indicate a way to get the proper files to
launch the gene-ontology search?
Thanks a lot.
--
Jean-Christophe Grenier, M.Sc.
-----------------------------------------
*Bio-informaticien*
*Laboratoire de Philip Awadalla*
*Laboratoire de Luis Barreiro*
*CHU Sainte-Justine*
3175, Côte Sainte-Catherine, local B-607
*Tél : 514-345-4931 poste 5199*
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