I'm trying to analyse my AFLP data using PeakSanner and RawGeno. When I get to the point in which RawGeno filters the low quality samples, I get a message that reads "Done, Check the working directory for a list of removed samples". According to the program only 56 out of 96 samples were kept, therefore there should be 40 removed samples. However, when I check the working directory, there is a file named "LostSamples" but it is empty. So, how do I know which samples were removed? And how do I know, in the image of the pseudo-gel which sample corresponds to each column? I mean, there are no names in the image...
I think the easiest way to do it is coding every sample so then you will know which ones are not taken into the analysis. I think RawGeno has limitations on providing all the information you want to check. For the pseudogel, I assume that the columns follow the ordering of the filtered samples. You can visualize the order of the samples if you create a binary database and export to excel or word.
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