I'm a bit confused between the information showing in webmaster tools vs analytics. Wemastertools shows 110,000 clicks through search queries Analytics shows 67,000 clicks. Which is correct? Thank you
Can't say which one tracks the best, are you sure the analytics code was installed properly on every page of the site?
yes if google analytics code will not install all pages of website it will not show in google analytics .. but webmaster will show it
install analytics code in footer of the site and then compare the result i'm sure both are accurate but your code is not installed on every page of your site
Check the dates. You'll notice Analytics is a rolling 30 days that you can adjust, and the last day was yesterday. Whereas webmaster tools is a predefined date period, that shows a 30 day cycle, that can be 1-3 weeks behind the data of analytics. Webmaster tools shows impressions, how many times your keywords were shown. It is hard to get clicks out of that data.
I do not think that you can compare both services. I mean both provides different features and google is also continuously interacting each others features....
Not only for your websites, this difference in numbers will be there for all the websites. It's true that since long time the difference is there and i go always go with Analytics data because i get the exact information of what i am looking from in GA and after certain improvements in Analytics i feel it is very easy.
Analytics based on javascript code you have placed on your pages. Webmaster tools based only on actions taken in google. They dont see clicks and queries from other SE. Also if you didnt put analytics code on every page you will not see all activities on you website.
I have found that they both produce pretty similar results so like the others have mentioned, look into your Analytics code.