Hi, We're integrating AMP-AD\_DiverseCohorts (syn51732482) with SEA-AD and MIT\_ROSMAP using a uniform CellBender -> SCTransform -> WNN pipeline. We'd like to request intermediate processing files that weren't uploaded to Synapse - ideally, the CellRanger ARC raw h5 outputs (per VR batch), and/or the post-CellBender h5 files, along with the freemuxlet donor assignments. Either level of processing would work for our purposes. This would save us from reprocessing 46 TB of FASTQs." Thank you in advance!

Created by Alperen Taciroglu AlpTaciroglu
Hi @vilasmenon, thank you very much for your willingness to help. I sent an email to your columbia.edu address.
Hi @AlpTaciroglu, thanks for the request. If you can send me an email, we can try to arrange a way to get the h5 files to you.
Hello! I am so sorry for the delayed response, this post slipped past me. We don't have this data on Synapse, but you can try contacting Vilas Menon at Columbia University ( @vilasmenon ) and see if he has these files available. I believe he is the original data contributor for this part of the data. I've tagged him here so hopefully he sees this and can respond directly.
Hi, just following up. I understand this may not be something that's available. If sharing these intermediate outputs isn't possible, that's completely fine - just knowing either way would help me plan my analysis. Thanks!

Request for intermediate CellRanger ARC / CellBender h5 outputs from AMP-AD_DiverseCohorts snMultiome (syn51732482) page is loading…