Dear team,
Regarding this data of Smart Seq2 in the MIT_ Rosmap_Multiomics, is it possible to have additional metadata information regarding the study, the number of individuals and cell barcodes etc? Is this information available?
Also, please confirm that the description of Data Processing in syn52558407 is related to the 10X droplet snRNA-seq and not related to the Smart Seq2 data.
Thanks.
Best regards,
Rajesh
Created by rrajesh Thanks! Hello @rrajesh,
Thanks for your questions. In case you haven't seen it, I would like to point you to the metadata files in syn52293430. To map the fastq files to this metadata, please view the file annotations that are present on each file. These can be found by clicking the `annotations` button on a given file, or accessed programmatically using the [Python](https://python-docs.synapse.org/reference/annotations/) or [R](https://r-docs.synapse.org/articles/synapser.html) client. These annotations contain specimenIDs and invididualIDs that you can use to map to the metadata files, and determine the number of individuals. Beyond this, I unfortunately don't have any information beyond what is in the metadata and study description.
As for your question about the Data processing description, I believe you are correct in that this corresponds to the 10x droplet snRNA-seq data found in syn52293442, as this description is also present in this folder, and the smartseq2 data would likely be processed with a different pipeline than Cellranger.
Best,
Will