I am trying to estimate the number of participants with different types of omics data in ROSMAP. I have used the different files provided in the Metadata folder. However, the specimen IDs are specific to each omics type (and thus there is no overlap between the files). There was a linker file before (ROSMAP ID key) to match the specimen IDs for each omics that is now indicated as deprecated. Would there be a similar file that we could use to assess the overlap? Thank you,

Created by CHLOE SARNOWSKI chloesar
Hi Ting, I think those missing RNAseq specimen IDs were uploaded as part of a different batch and do not have associated BAM files. However, I think those specimens have fastq files here: [https://www.synapse.org/#!Synapse:syn21589959](https://www.synapse.org/#!Synapse:syn21589959). Abby
Dear Abby, Thank you for your reply. It is very clear. I can get all the WGS VCF samples. BTW, "syn22333035" seems not to include all the RNA-seq samples; ~90 RNA-seq samples were not included in "syn22333035". Is this also because of the mismatched ID? For example, I can not find bam files for RNA-seq ID "RISK_237", "RISK_238_redo", "RISK_241_rerun" etc. Thank you, Ting
Hi Ting, The 45 sample IDs in the VCF files that do not match the biospecimen metadata are from the ROSMAP cohort and have an old naming convention that includes 'ROS' or 'MAP' as a prefix. You can join these 45 missing samples to the 'projid' column in the [ROSMAP clinical metadata file](https://www.synapse.org/#!Synapse:syn3191087). The numeric portion of the sample ID without the ROS or MAP prefix should match one of the projids in the clinical file, and from there you can find the individualID that is used in the other WGS metadata files. I will work on providing additional information in the WGS metadata so these samples from the VCF can be correctly mapped without having to go through these extra steps, but it may take me a while to get to. Apologies and let me know if this solution works for you in the meantime! Best, Abby
A follow-up question: There were 1196 whole-genome sequencing (WGS) samples with VCF files (syn11707419); and "biospecimen metadata" file actually lists 1196 "specimenID" with the WGS assay; "ROSMAP_assay_wholeGenomeSeq_metadata.csv" file (syn21314542) also lists 1196 samples. However, there are 45 individuals in "WGS" VCF files (syn11707419) that do not match Metadata of genotype (syn21314542). For example, sample ID "MAP15387421" in the WGS VCF file does not exist in Metadata of genotype. Is there a way to link the relationship for these 45 samples between WGS VCF files and WGS Meta data files? Thank you.
Thank you for your quick answer! This is indeed what I ended up doing. Great to have confirmation from you. Best, Chloé
Hi Chloe, The updated [biospecimen metadata file](https://www.synapse.org/#!Synapse:syn21323366) for the ROSMAP study actually lists each specimenID with the assay it was used in and the individualID it belongs to. You can use this file to check which individuals appear in which assay, which should let you know which types of omics data are available for each participant! Let me know if this isn't what you're looking for. Best, Abby

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