Hello,
Thank you for taking my inquiry. I have been able to download and re-map the 10 scRNA microglia samples from the ROSMAP study.
I am also trying to re-map/quantify the same 10 bulk RNA (DLPFC) samples, which are available in BAM format.
The meta file that accompanies the scRNA contains the 'projid'; however, I am unable to relate the 'projid' to the BAM (sample). Is this possible?
Thanks and be well!
Created by John Malamon jmal0403 That's very helpful -- thanks!
The 'individualID' annotations on the ROSMAP BAM files will allow you to link between the bulk RNA BAM and the microglia RNAseq files.
Working with the table you're already using, view files where study = 'ROSMAP', assay = 'RNAseq', cellType = 'Not set', and fileFormat = 'bam' and then use the advanced query feature to limit those results to the individualIDs from the microglia RNAseq files. For an abbreviated example, the query and link below give BAM files associated with two of those individualIDs: R6928327 and R9938478.
If this doesn't answer your question, please let me know!
SELECT study, dataType, assay, id AS file_id, specimenID, individualID, diagnosis, sex, consortium AS "Program", grant, species, organ, tissue, cellType, fileFormat FROM syn11346063 WHERE ( ( "study" = 'ROSMAP' ) AND ( "assay" = 'rnaSeq' ) AND ( "cellType" IS NULL ) AND ( "fileFormat" = 'bam' ) AND "individualID" IN ('R6928327', 'R9938478'))
https://www.synapse.org/#!Synapse:syn11346063/tables/query/eyJzcWwiOiJTRUxFQ1Qgc3R1ZHksIGRhdGFUeXBlLCBhc3NheSwgaWQgQVMgZmlsZV9pZCwgc3BlY2ltZW5JRCwgaW5kaXZpZHVhbElELCBkaWFnbm9zaXMsIHNleCwgY29uc29ydGl1bSBBUyBcIlByb2dyYW1cIiwgZ3JhbnQsIHNwZWNpZXMsIG9yZ2FuLCB0aXNzdWUsIGNlbGxUeXBlLCBmaWxlRm9ybWF0IEZST00gc3luMTEzNDYwNjMgV0hFUkUgKCAoIFwic3R1ZHlcIiA9ICdST1NNQVAnICkgQU5EICggXCJhc3NheVwiID0gJ3JuYVNlcScgKSBBTkQgKCBcImNlbGxUeXBlXCIgSVMgTlVMTCApIEFORCAoIFwiZmlsZUZvcm1hdFwiID0gJ2JhbScgKSBhbmQgaW5kaXZpZHVhbElEIGluICAoJ1I2OTI4MzI3JywgJ1I5OTM4NDc4JykpIiwgImluY2x1ZGVFbnRpdHlFdGFnIjp0cnVlLCAiaXNDb25zaXN0ZW50Ijp0cnVlLCAib2Zmc2V0IjowLCAibGltaXQiOjI1fQ==
Hi Meagan,
Thanks for the quick response. Sure, here is a link to the list of scRNA subjects (n=10, files=40)
https://www.synapse.org/#!Synapse: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
The query results provide the 'specimenID' and the 'individualID' for the 10 samples. I want to find the corresponding bulk RNA BAM files for these 10 subjects.
Here is a link with the bulk RNA BAMs:
https://www.synapse.org/#!Synapse:syn4164376
I am failing to see how to link the two sets of IDs.
Hope this helps. Thanks!
Hello,
Could you please let us know the Synapse IDs of the files/folders you're referring to? That will help us look into your question.
Thanks!
Drop files to upload
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