I am working with some of the datasets posted to the brain atlas. We would like to use them while developing a computational technique for denoising single cell data.
We are having some issues with the Human Multiple Cortical Area SMART-seq dataset and would like to
- know where it has been published, if anywhere, so that we may follow along from there - at first glance it appears to be from Hodge et al. 2019, however the number of cells does not match up,
- know if the preprocessing and filtering has already been done to the data. The criteria posted on the Allen brain atlas page do not appear to be immediately enforceable given the data we are given (a count matrix),
- identify whether it is possible to obtain or process count matrices that merge the introns and exons, as well as only consider the introns, and only consider the exons. As it stands it is unclear from the reference genome what are considered introns vs. lncRNAs.
I appreciate your time.
Jay S. Stanley III