First, since it is my first post here, thank you for sharing this great dataset! I have been looking at the quality control metrics (syn8698270, syn8698214, syn8698211, syn8698240) and found there is a batch of 87 MSBB samples with > 99% aligned reads (see https://www.synapse.org/#!Synapse:syn18428603, the batch on the right). This seems to be very high, also when you compare it to the other AMP-AD samples, which are processed in the same way. Do you have an idea of why these samples have such high alignment rates? Is there a difference in sample preprocessing that can explain this?

Created by Niek de Klein NiekdeKlein
Hi @NiekdeKlein The MSBB data is from single end RNA-Sequencing so higher alignment rates are expected compared to ROSMAP and Mayo.
We are actively looking into this now, and will let you know what we find. Thanks, Ben
Hi Niek, Thanks for pointing that out! We will have to dig in a little deeper on this, we will try to get back to you in the next four weeks to see if we can sort out what's going on here. Ben

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