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rdpstaff / classifier

RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
GNU General Public License v2.0
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copy number file -c flag #11

Open complexgenome opened 9 years ago

complexgenome commented 9 years ago

Hello classifier team, I'm interested to use copy number utility from RDP classifier. I've following as my query: 1- The documentation mentions to provide copy number files with flag -c. However, in -help, -c is for the confidence used for the classification. Am I misunderstanding something from help on IO screen and your documentation? Kindly guide.

rdpstaffmsu commented 9 years ago

Hi, Sanjeev,

'-c' option takes copy number file when Classifier is in 'train' mode, e.g. 'java -jar classifier.jar train', while it means confidence in 'classify' mode. Let me know you have questions.

Benli

On Fri, Aug 14, 2015 at 10:20 AM, Sanjeev notifications@github.com wrote:

Hello classifier team, I'm interested to use copy number utility from RDP classifier. I've following as my query: 1- The documentation mentions to provide copy number files with flag -c. However, in -help, -c is for the confidence used for the classification. Am I misunderstanding something from help on IO screen and your documentation? Kindly guide.

— Reply to this email directly or view it on GitHub https://github.com/rdpstaff/classifier/issues/11.

RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

complexgenome commented 9 years ago

Hi Benli,

Thanks. --Sariya

rdpstaffmsu commented 9 years ago

This option is used only when you re-train the Classifier. You can also contact us through rdpstaff@msu.edu email.

Benli

On Fri, Aug 14, 2015 at 12:22 PM, Sanjeev notifications@github.com wrote:

Hi Benli,

  • Thanks for your prompt response.
  • Can I use -c (copy number flag) with default RDP classification? Or is it to be used with trained data set, only?
  • Is there a mailing list for queries to RDP? Or would you suggest me to go ahead and ask at github?

Thanks. --Sariya

— Reply to this email directly or view it on GitHub https://github.com/rdpstaff/classifier/issues/11#issuecomment-131167713.

RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

complexgenome commented 9 years ago

Hi Benli, Thanks for sharing mail id. I've contacted the mentioned mail for further doubts. Reply much awaited. :-) Regards, Sanjeev