Hello, I have get access to ROSMAP multi-omics data, but there But there are still some problems bothering me? such as: How to dowload the RAW BAM/FASTQ files? How I can kown the detailed information of each BAM/FASTQ files, for example, it was from control or MCI or AD ? I look forward to your help and advice @Mette Thanks! Best Regards!

Created by Junjie Shao JunjieShao202205162100
Hi abby, Thank you very much! Best wishes for you! @@abby.vanderlinden
Hi Junjie, Oh I see, you are trying to get data from the Progenitor Cell Biology Consortium Portal, rather than the AD Portal. Regardless, your command line should be: ` synapse get -q "SELECT * FROM syn7511263 WHERE dataType = 'mRNA' AND fileType = 'fastq' AND Cell_Type_of_Origin = 'CD34+ cells'" ` You can actually use the facets or the SQL query bar in the syn7511263 table to filter the table how you want, and then click the "Download Options" arrow icon on the top right of the table, select "Programmatic Options", and copy the provided command line, R, or python command to download exactly the files you have selected. Let me know if that works!
Hello Abby, There is something wrong with my command line, but I am confused where the error is, Can you help me? The command line that I used as following: synapse query 'select * from syn7511263 where dataType="mRNA" AND fileType="fastq" AND Cell_Type_of_Origin="CD34+ cells"' The error is: Unknown column 'mRNA' in 'where clause' Note: If a column name contains spaces, punctuation, or SQL key words, then the name must be enclosed in double quotes. But the mRNA was enclosed in double quotes as quotes, I don't know where the mistake is. Regards, wishes for you! @abby.vanderlinden Junjie Shao
Hello Abby, I really appreciate your kind help! I will try my best to do it according to your advise. And I will contact you if there is any additional questions! Regards, Best wishes for you! @abby.vanderlinden Junjie Shao
Hi there, You can find more information on how to download files from the AD Knowledge Portal in bulk [here](https://help.adknowledgeportal.org/apd/Use-Case-%232:-Download-Files-in-Bulk-Using-the-Command-Line-Client.2426503243.html). Individual, biospecimen, and assay metadata for all data files are included as flat csv files that accompany each study, and can be joined to data files as described [here](https://help.adknowledgeportal.org/apd/Use-Case-%233:-Working-with-File-Annotations-and-Metadata.2426208334.html). The ROSMAP [clinical metadata file](https://adknowledgeportal.synapse.org/Explore/Data?QueryWrapper0=%7B%22sql%22%3A%22SELECT%20*%20FROM%20syn11346063.25%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22study%22%2C%22facetValues%22%3A%5B%22ROSMAP%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22resourceType%22%2C%22facetValues%22%3A%5B%22metadata%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22dataType%22%2C%22facetValues%22%3A%5B%22clinical%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22metadataType%22%2C%22facetValues%22%3A%5B%22individual%22%5D%7D%5D%7D) contains information on Braak stage, CERAD score, and cognitive diagnoses for each individual, which can be used to categorize cognitive impairment based on your preferred criteria. The ROSMAP [clinical codebook](https://adknowledgeportal.synapse.org/Explore/Data?QueryWrapper0=%7B%22sql%22%3A%22SELECT%20*%20FROM%20syn11346063.25%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22study%22%2C%22facetValues%22%3A%5B%22ROSMAP%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22resourceType%22%2C%22facetValues%22%3A%5B%22metadata%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22dataType%22%2C%22facetValues%22%3A%5B%22clinical%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22metadataType%22%2C%22facetValues%22%3A%5B%22data%20dictionary%22%5D%7D%5D%7D) describes the variables in the metadata file. Let me know if this helps -- happy to answer any additional questions! Abby

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