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Created by Kenneth Daily kdaily @kdaily Dear Kenneth,
Could you please tell me what's the annotation database used for RNASeq data? and the genome version?
Thanks a lot in advance,
Jianmin Please see this page for the available metadata tables: https://www.synapse.org/#!Synapse:syn1773109/wiki/218832. Most of this information is also included as annotations on the files themselves. This is the only metadata we have available. [This table](syn2767694) specifically (syn2767694) has the metadata about the cell lines. @kdaily Thank you very much. this is very helpful. I would like to analyse possible relations between geno features such as biomarkers, variants and clinical metrics like cancers, survival outcomes. Do these geno files have any clinical data for them? thanks. You're welcome! You can read more about downloading here:
- https://docs.synapse.org/articles/downloading_data.html
- https://docs.synapse.org/articles/uploading_in_bulk.html#downloading-data-in-bulk
@kdaly Thanks, this is great. Can you have example of how to download a bam file? @z160896 ,
This table (syn7511263) lists all of the C4 data files. It uses a slightly different query syntax than the one you have. Your query (minus the `Originating_Lab_ID`, I'll have to check why that is not available) would be:
```
select id,name,Originating_Lab,C4_Cell_Line_ID FROM syn7511263 WHERE ( ( "dataType" = 'Karyotype' ) )
```
In Python you would do:
```python
import synapseclient
syn = synapseclient.login()
query = 'select id,name,Originating_Lab,C4_Cell_Line_ID FROM syn7511263 WHERE ( ( "dataType" = \'Karyotype\' ) )'
results = syn.tableQuery(query)
results.asDataFrame() # Requires that you have pandas installed
```
Here's what that query result would look like, or you can visit this [url](https://www.synapse.org/#!Synapse:syn7511263/tables/query/eyJzcWwiOiJzZWxlY3QgaWQsbmFtZSxPcmlnaW5hdGluZ19MYWIsQzRfQ2VsbF9MaW5lX0lEIEZST00gc3luNzUxMTI2MyBXSEVSRSAoICggXCJkYXRhVHlwZVwiID0gJ0thcnlvdHlwZScgKSApIiwgImluY2x1ZGVFbnRpdHlFdGFnIjp0cnVlLCAiaXNDb25zaXN0ZW50Ijp0cnVlLCAib2Zmc2V0IjowLCAibGltaXQiOjI1fQ==) to see the results:
${synapsetable?query=select id%2Cname%2COriginating%5FLab%2CC4%5FCell%5FLine%5FID FROM syn7511263 WHERE %28 %28 "dataType" %3D %27Karyotype%27 %29 %29 &showquery=true}
Hi @z160896 ,
Apologies, but that query uses a Synapse service that no longer exists. Could you let me know where in the documentation that you read this? I will get back to you shortly with the appropriate query. Hello, I try to test this query in Python Synapse Client: 'select id,name,Originating_Lab,Originating_Lab_ID,C4_Cell_Line_ID from file where projectId=="syn1773109" and dataType=="Karyotype"'. I got this error: ValueError: Couldn't extract synapse ID from query: "select id,name,Originating_Lab,Originating_Lab_ID,C4_Cell_Line_ID from file where projectId=="syn1773109" and dataType=="Karyotype"". Is this ID, syn1773109, still valid. Thanks Thank you! Jungsun Hello, thanks for the report. I also see that the data explorer is not properly loading data. I will have to debug it to determine what could be the issue.
The data explorer does very little processing of it's own - only filtering and selecting of appropriate genes, miRNAs, and metadata. All of the data used is already processed and available in this project. The code that runs the data explorer is publicly available, but documentation is sparse. If you are familiar with R Shiny applications, you might be able to determine the processing.
https://github.com/Sage-Bionetworks/PCBCDataExplorer
Dear Kenneth,
I analyzed my RNA-seq data using the "interactive data explorer" back in 2016 and working on a manuscript. I am going to cite "Salomonis, et al. Stem Cell Reports, 2016" in my manuscript. To find out the detailed script/parameter, I have revisited this explorer but I cannot access the "Interactive Data Explorer". I assume that my computer may not be compatible with this explorer. Would you please help me to sort out this issue? Alternatively, I can download the raw data and process if you are able to share the scripts that you used for interactive data explorer.
Thanks a lot in advance,
Jungsun