Hello,
I've been attempting to find the metadata file that corresponds with the sample name identifier of the fastq samples in syn8612097 but I could not find it. Can someone possibly direct me to where this metadata is located? I 've been comparing with the metadata csv file in syn3191087 but the identifiers don't correspond with each other. Any help with this would be most appreciated,.
Thank you,
Christian
Created by Christian Perez cmiperez Dear Abby,
Thank you for your kind reply. It is very helpful. Now I can find bam/fastq files for most of the samples listed in Metadata. However, it seems that these 10 RNA-seq samples do not have bam or fastq files.
for example, specimenID = "R9938478"; "R9254359" etc. Am I missing something? Thank you in advance.
Best Wishes,
Ting @echoqiting
Hi Ting,
Here is an [AD Portal query](https://adknowledgeportal.synapse.org/Explore/Data?QueryWrapper0=%7B%22sql%22%3A%22SELECT%20*%20FROM%20syn11346063%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%22assay%22%2C%22facetValues%22%3A%5B%22rnaSeq%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22tissue%22%2C%22facetValues%22%3A%5B%22dorsolateral%20prefrontal%20cortex%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22fileFormat%22%2C%22facetValues%22%3A%5B%22bam%22%2C%22fastq%22%5D%7D%5D%2C%22additionalFilters%22%3A%5B%5D%7D) that pulls all ROSMAP rnaSeq bam and fastq files from the DLPFC tissue (891 bam and 542 fastq files). You should be able to map the specimenIDs and individualIDs from the biospecimen metadata to these files -- for example, I checked for specimenID = 1026-DLPFC in this query, and found a bam file for it.
You can use the "Download Options" arrow at the top of the Portal query table to construct a programmatic download command, or follow the links from the data files back to Synapse if you prefer. Does this help you find what you need?
Abby Hi there,
I am analysis RNAsey data from Mayo RNAseq, both temporal cortex and cerebellum. But I need to know which part of temporal cortex and cerebellum were exactly used for this dataset?
Unfortunately, I could not find any detail through synapse metadata or corresponding paper. Could someone help me out?
Best,
Tima Dear Abby,
A follow-up question about the ROSMAP RNA-seq individual data files:
I downloaded 698 fastq files from "syn21589959", and 639 bam files from "syn4164376".
In the ROSMAP biospecimen metadata, there were ~900 RNA-seq samples from "dorsolateral prefrontal cortex".
However, it seems that not all the 900 RNA-seq samples have fastq or bam files in syn21589959 or syn4164376.
Where can I find RNA-seq bam or fastq files for the other samples (e.g., R2809589, 1026-DLPFC )?
Thank you in advance!
Ting
Thank you very much Abby this helps clarify my confusion. If I run into anymore issues I will be sure to let you know.
Best,
Christian Hi Christian,
The fastq file names include the specimenID for each sample, which can be found in the [ROSMAP biospecimen metadata here](https://www.synapse.org/#!Synapse:syn21323366). The biospecimen file maps each specimenID to an individualID, which can then be joined to the individual metadata in the ROSMAP clinical file that you linked to.
The annotations on the fastq files also include a specimenID annotation, although these annotations appear to have an extra underscore and digit following the specimenID as seen in the biospecimen file (e.g., the file is annotated with specimenID = 01_123456_02, but the biospecimen file specimenID = 01_123456). I think this probably has to do with some metadata harmonization and standardization that has taken place recently. Until we get the annotations fixed, you should still be able to match the fastq file names or the first portion of the specimenID file annotations with the biospecimen metadata.
Let me know if you run into any other issues!
Best,
Abby
Drop files to upload
syn8612097: Metadata for ROSMAP FASTQ Files page is loading…