Recently, the data were reprocessed in parallel with other AMP-AD RNAseq datasets, and this second version of the data are available as well. The input data for the RNAseq reprocessing effort was aligned reads in bam files that were converted to fastq using the Picard SamToFastq function. Fastq files were re-aligned to the GENCODE24 (GRCh38) reference genome using STAR with twopassMode set as Basic. Gene counts were computed for each sample by STAR by setting quantMode as GeneCounts, and transcript abundance estimated using Sailfish (see https://www.synapse.org/#!Synapse:syn9702085/ for details).
