I purchased my first Kobo about 6 weeks ago. Like you I also decided on the Libra 2. I was a bit hesitant at first as I had always used a Kindle, but I was a bit frustrated with the Kindle as it was impossible to sort books into lists useful to me.
Now I have absolutely no regret with the Kobo. I have been able to set it up exactly as I want with Sets and Collections that are useful to me and davidfor above was really helpful with me achieving that goal.
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Originally Posted by PunkyKoopa
I have about 20 or so books in my Amazon account. I wonder if I should switch to Kobo Store and start to get my books from there or start using Calibre.
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I haven't. I still use my Amazon account. I have well over a hundred books on Amazon, and I was still able to get them onto the Kobo.
I use Calibre along with DeDRM and I have installed the Kindle for PC software.
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Originally Posted by PunkyKoopa
-I need the deDRM plugin. The only thing that I have to configure is my Kindle serial number, right?
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Yes.
When you download the plugin, remember the install zip file is in the downloaded file, so you have to extract it out.
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Originally Posted by PunkyKoopa
-Should I use Kobo Touch Extended Driver and convert to Kepub instead of ePub? What are the main differences? I like the more advanced options to customize fonts, sides and margins of Kobo versus Kindle, so I don't want to miss anything here.
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I don't use kepub, only epubs. And I am happy with the result.
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Originally Posted by PunkyKoopa
-Will I miss features if I continue to get my books from Amazon and then convert with Calibre? I like to have reading stats to sett my trends, remaining time or pages...I also use A LOT highlights and dictionary with my Kindle.
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Yea, that is the only downside. Previously I could read in bed on my Kindle, on the train on my iPhone, or out and about on my iPad. Now that is not possible and I have to carry the Libra 2 around with me.
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Originally Posted by PunkyKoopa
-Just to sum up, will be any difference between the same book from Kobo Store to a side loaded book from Amazon? Side loaded books will have any weird restrictions or wrong margins and spacing due to conversion?
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As another member stated here in another thread, sometimes you can get great books from Amazon, with great formatting, other times it can be full of crap. So far I have come across a few books from Amazon that needed cleaning up due to inconsistent formatting.
As for the Kobo store, I have no idea as I haven't purchased from them yet. But I would imagine the publisher is uploading the same book to these retailers.