SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
coomercial or open source tool for CNV from sequence data mathew Bioinformatics 5 08-26-2012 10:15 AM
Recommendation for CNV detection software in Illumina WGS data for cancer cells yuhao Bioinformatics 4 08-15-2012 08:42 AM
Which technology is better for CNV detection, SOLiD or Solexa? El Mariachi SOLiD 0 12-30-2010 12:45 AM
CNV detection via BAM depth-of-coverage quinlana Bioinformatics 4 09-10-2010 04:58 AM

Reply
 
Thread Tools
Old 10-25-2012, 03:16 AM   #1
Malobi
Junior Member
 
Location: New Delhi, India

Join Date: Oct 2012
Posts: 1
Default CoNIFER:CNV detection tool

I am trying to run conifer and not sure about the SVD normalization like how its is done. How the sample amount effects the analysis quality. what does removal of svd components mean. while calling CNV how on what basis do we set the threshold value? How can we measure the sensitivity and the specificity of the result.
Malobi is offline   Reply With Quote
Old 10-31-2013, 05:09 AM   #2
omerfaruk
Member
 
Location: Turkey

Join Date: Apr 2013
Posts: 18
Default

You could decide svd value after the first run, looking at the scree plot.

The higher the control size the merrier
omerfaruk is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:19 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO