Hi, I am trying to get bulk DLPFC RNAseq (from syn3505720) using the specimen IDs (from syn21323366) specimen IDs I am interested in are not in present in syn3505720. For example, the specimen ID for DLPFC bulk cell RNAseq for the individual RXXXXX is XXXX-DLPFC, but there is no such ID in syn3505720 (X being some number). Is there a way for me to get the bulk RNAseq for these specimen whose ID's don't follow the convention used in the dataframe? I appreciate any help you can provide. Thanks, Juan

Created by Juan Sepulveda juansep99
Hi Abby, Thank you so much for your help! I was able to find the cohort of interest in the harmonization study. But I am unfamiliar with CQN and have a follow-up question: Are the gene counts in ROSMAP_Filtered_counts_(greater_than_1cpm).tsv (syn26967451) already normalized? From what I understand, the contents of ROSMAP_Normalized_counts_(CQN).tsv (syn26967453) are the offset values, and to apply the normalization, I should subtract the offset from the counts. But I don't know if the offset has already been subtracted from the gene counts. Thanks, Juan
Hi Juan, For the ROSMAP bulk RNAseq, we recommend using the counts from the RNASeq Harmonization study (syn21241740). The original counts included in the ROSMAP folder are quite old, whereas the harmonized counts are aligned to GRCh38 and include filtered and CQN-normalized matrices. The harmonized counts should have specimenIDs that match the ROSMAP biospecimen metadata. If for some reason you specifically need to use the original ROSMAP counts that were generated in 2015, there is an old ID key file that will map the column headers in that counts file to the ROSMAP projids (found in the clinical metadata) via the "rna_id" column: syn3382527. Let me know if that helps -- happy to answer any additional questions. Abby

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