[Cg-pipeline-users] pipeline question

[Matthew S. <ms...@la...>]

Hello,

 

We have installed the pipeline locally, and I was wondering if you could
answer a couple of questions

 

First of all, I have noticed two or three issues with the annotation.gbk
file.

 

Firstly, the naming structure for the organism.  Is there a defined
structure that must be entered into the cgpipelinerc file to make the name
show up appropriately in the entries?  (it defaults to nesseceria, and to
change it for viruses, for example, I would like to know what the structure
is)

 

Second, It is exceedingly difficult from first glance to determine if an ORF
has been assigned a function/homology, or is simply an identified ORF.  Is
there any way to modify the write-out to make this distinction more obvious?

 

Third, I have been attempting to find a way to have annotated genes write
out the functional name to the gbk file, rather than simply the gene_id as
it does now.

 

Also, I was unclear as to why there are two cgpipelinerc files (one in the
conf directory and one in the lib directory). 

 

Thank you,

 

____________________________

Matthew Scholz

GRA-Los Alamos National Laboratory

ms...@la...

(505) 665-8574