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I have to run an analysis using Whole Exome Sequencing (WXS) data prepared with the TruSeq Exome Kit (2012).

I need the .bed file for the kit and I found it here.

However, this file was posted on Nov. 16, 2015, while the kit used in my case is from 2012. I searched but I didn't find the bedfile for that specific version online.

Will I run into problems if I use this version, and in this case, where can I retrieve the bedfile for 2012's version?

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  • $\begingroup$ Care to explain why the downvote? $\endgroup$ – gc5 Nov 17 '17 at 15:29
  • $\begingroup$ I haven't down voted you, but you don't show what have you done to understand what problems can you have when using an older file, nor the places you have searched for the bed files of 2012. Or maybe it was from biology.se, who knows ? $\endgroup$ – llrs Nov 17 '17 at 15:36
  • $\begingroup$ I usually search before writing a question, so also in this case I searched online to understand what could be the difference. Since online I couldn't find anything I wrote this question. Also, the fact that I put the reference to the Illumina kit page (the only page in which I could find reference to the bedfile of the kit) disproves that I didn't put the places I have searched. So I don't see the point of downvoting, since I: clearly stated the problem, provided details about what I've done, provided links to what I've found. $\endgroup$ – gc5 Nov 17 '17 at 15:44
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    $\begingroup$ Well, those are imaginary internet points, don't mind them too much! $\endgroup$ – llrs Nov 17 '17 at 16:04
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    $\begingroup$ Actually I don't mind them :) but since I put some effort to search and write I couldn't understand why the downvote. $\endgroup$ – gc5 Nov 17 '17 at 16:15
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Usually it is more problematic to work with older versions of data with newer protocols than the other way around.

In this case, I think that the features annotated in the (newer) bed file should be more accurate than the older one. Unless you specifically want to compare your experiment with a previous experiment performed with a bed file from 2012 you'll be fine using the newer one.

However make sure that you are correctly using the right file and that you report (or record) each version of protocol and data used in case some doubts arise.

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