As titled, I noticed that the folder syn21589959 contains 698 files corresponding to 349 subjects with specimen IDs that start with "RISK_." However, I did not find any descriptions of these files in Synapse or in the corresponding paper titled "A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer?s disease" (Mostafavi, S., Gaiteri, C., Sullivan, S.E. et al. 2018).
I was wondering if there is a resource that details these fastq data?
Additionally, I was also wondering if the preprocessing code that transforms the BAM files to FPKM data from the aforementioned paper (Mostafavi, S., Gaiteri, C., Sullivan, S.E. et al. 2018) is posted anywhere on Synapse? If so, where can I request access?
Thank you!
Created by l13achen @Mette or @annagree Do you know of any publications related to the ROSMAP "RISK_" (third batch) of bulk RNAseq data?
Hi Abby!
Thank you for the information! I just wanted to follow up and ask if there are any publications regarding the "RISK_" files. Any further information about the origin, analysis, or results from the files? I've searched online but can't seem to find any. If you could direct me to some resources, that would be lovely!
Thank you!
Lisa Hi there, the "RISK_" files were generated in 2020, after the publication of the paper detailing the network analysis. In the folder wiki methods section for the bulk brain RNAseq, the library preparation and sequencing details for "batch 3" correspond to these RISK files. In the ROSMAP RNAseq assay metadata file, there's a "notes" column that indicates which "data submission batch" (1, 2, or 3) a specimen was part of.
I don't believe we have the preprocessing code used to process the BAM files from the first two data submission batches referenced in the paper -- I would recommend contacting the paper authors to request that.
Let me know if you have any other questions!
Abby
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