SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Newbie Question: Calculating physical coverage from genome coverage tristanstoeber Illumina/Solexa 4 06-24-2013 11:53 AM
calculating the coverage over a gene kjaja Bioinformatics 3 06-01-2012 07:01 AM
calculating the coverage lyz1030 Bioinformatics 3 04-03-2012 06:03 PM
what program can i use for calculating coverage? dkrtndhkd Bioinformatics 2 02-03-2012 06:39 PM
Gene list for calculating coverage nseh Bioinformatics 1 05-22-2011 07:31 AM

Reply
 
Thread Tools
Old 12-08-2012, 09:33 AM   #1
tahamasoodi
Success
 
Location: India

Join Date: May 2012
Posts: 130
Default Calculating sequence coverage

How can we calculate the coverage of Illumina paired end whole genome sequencing data using Waterman equation? Example data is given:

Total reads = 450,000,000
Read length = 101
Genome size = 3000000000
__________________
Thanks,
tahamasoodi is offline   Reply With Quote
Old 12-08-2012, 09:53 AM   #2
lorendarith
Guest
 

Posts: n/a
Default

http://www.illumina.com/Documents/pr...alculation.pdf

The Lander/Waterman equation is a method for computing coverage.
The general equation is:

C = LN / G

• C stands for coverage
• G is the haploid genome length
• L is the read length
• N is the number of reads

So, if we take one lane of single read human sequence with v3 chemistry, we get

C = (100 bp)*(18910^6)/(310^9 bp) = 6.3

This tells us that each base in the genome will be sequenced between six and seven times on average.

---------------------

Though take care whether the "total reads" number is really the number of all reads (read 1 + read 2) or actually the "total pair" number. In the first case, you can just do the equation, however if it's the latter then you need to

C = 2*LN/G

Last edited by lorendarith; 12-08-2012 at 10:03 AM.
  Reply With Quote
Old 12-08-2012, 10:28 AM   #3
tahamasoodi
Success
 
Location: India

Join Date: May 2012
Posts: 130
Default

How can we know whether it is total number or paired number?
__________________
Thanks,
tahamasoodi 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 12:33 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO