SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
vcfutils.pl -specifying minimum read depth? Lspoor Bioinformatics 3 05-27-2013 01:20 AM
varFilter -D (maximum read depth) usage sehrrot Bioinformatics 0 06-23-2012 10:22 PM
Maximum read Depth in Samtools Anjali Bioinformatics 2 01-16-2012 02:15 AM
How to decide maximum read depth in Samtools VarFilter Muhua wang Illumina/Solexa 0 10-06-2011 03:02 PM
What's maximum depth and minimum depth? slny Bioinformatics 0 03-17-2011 10:13 AM

Reply
 
Thread Tools
Old 05-28-2013, 04:34 PM   #1
eleven
Junior Member
 
Location: China

Join Date: Jan 2013
Posts: 9
Smile minimum and maximum CNV size by Read Depth?

Hello! everyone.

Read depth (RD) is a good method to detect CNV. Generally, CNV size by RD is not large as far as I know, also depends on pre-selected bin size such as 100bp or 500bp. So has someone known RD methods very well and what is the minimum and maximum CNV length approximately?

Thanks a millionaire
eleven is offline   Reply With Quote
Old 05-28-2013, 04:54 PM   #2
JackieBadger
Senior Member
 
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381
Default

I am not sure if you are using the correct terminology or explaining your question very clearly. CNV relates to the estimated copy number of genes.... when alleles are indistinguishable in sequence at duplicated loci, RD is used to estimate the CNV based on sequence depth i.e. the number of sequences is some quantification of the number of loci. Sequence length is not used as a measure of CNV.

Are you asking what are the best method to detect CNV using RD?
If so..it is a burgeoning field.
JackieBadger is offline   Reply With Quote
Old 05-29-2013, 01:36 AM   #3
eleven
Junior Member
 
Location: China

Join Date: Jan 2013
Posts: 9
Default

sorry for replaying you so late! I may be confused about conception, so thank you!
eleven is offline   Reply With Quote
Reply

Tags
cnv, read depth

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 05:18 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO