I am writing to get some help with downloading the training data for the multiple myeloma challenge study: syn6187098.
On the synapse portal, molecular data file I see is 'MMRF_VCF_from_RNA-Seq.tar.gz?, however I cannot seem to find links for the 823 patient cohort study, as mentioned in the webinar.
RNAseq: 658
WES variants: 764
I was wondering if you could please point me to the location from where I could download the molecular (raw sequencing) and patient outcome data files for the training set?
Appreciate all the help.
Created by sgujja Hi Mike,
Can you help with the error below from running the python script:
I've not used the actual synapse id in the command below:
chal_data_table = syn.tableQuery('select id, name from syn9748391')
Traceback (most recent call last):
File "", line 1, in
File "/Users/sgujja/anaconda3/lib/python3.7/site-packages/synapseclient/client.py", line 2752, in tableQuery
return CsvFileTable.from_table_query(self, query, **kwargs)
File "/Users/sgujja/anaconda3/lib/python3.7/site-packages/synapseclient/table.py", line 1582, in from_table_query
includeRowIdAndRowVersion=includeRowIdAndRowVersion)
File "/Users/sgujja/anaconda3/lib/python3.7/site-packages/synapseclient/client.py", line 2910, in _queryTableCsv
download_from_table_result = self._waitForAsync(uri=uri, request=download_from_table_request)
File "/Users/sgujja/anaconda3/lib/python3.7/site-packages/synapseclient/client.py", line 2611, in _waitForAsync
async_job_id = self.restPOST(uri+'/start', body=json.dumps(request), endpoint=endpoint)
File "/Users/sgujja/anaconda3/lib/python3.7/site-packages/synapseclient/client.py", line 3346, in restPOST
exceptions._raise_for_status(response, verbose=self.debug)
File "/Users/sgujja/anaconda3/lib/python3.7/site-packages/synapseclient/exceptions.py", line 153, in _raise_for_status
raise SynapseHTTPError(message, response=response)
synapseclient.exceptions.SynapseHTTPError: 400 Client Error:
unknown table type: project
Can you please help.
Thanks Dear SGujja,
I would recommend working with the most recent version of MMRF COMMPASS data (IA12) which is not actually part of the Multiple Myeloma DREAM Challenge dataset (where MMRF IA9 was used). You can find it [here](https://research.themmrf.org/) under the downloads tab after signing up and gaining access, which takes about a day. The 823 sample count resulted from the union of of the 658 RNA-seq and 764 WES data in the IA9 data release. The intersect, which I believe is much lower, should have increased in the latest IA10 release.
Drop files to upload
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