SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Can BSMAP calculate the coverage/ percentage of all CpGs covered in the reference? illuminaGA Bioinformatics 4 04-25-2016 01:53 AM
Calculating percent covered per chromosome mlodato Bioinformatics 4 10-25-2013 02:36 PM
Percentage of exons covered meher Bioinformatics 8 06-26-2013 04:31 AM
Sequencing all for the diagnosis--now it's even covered. Joann Literature Watch 0 03-03-2011 10:03 AM

Reply
 
Thread Tools
Old 05-12-2015, 02:07 AM   #1
Hparker
Member
 
Location: UK

Join Date: Dec 2014
Posts: 42
Default number of CpGs covered

Hello All,

I have bisulfite sequencing data from the SeqCapEpi protocol from NimbleGen/Roch and I am beginning to analyse my data. I aligned using Bismark/bowtie2 and I'm using Unix and R to analyse the data. I would like to create a simple table to show the total number of reads and total number of CpGs and number of CpGs with at least 10x coverage. Please could you let me know how I would determine the number of CpGs in each of my samples?

Many thanks!
Hparker 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 03:44 AM.


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