#Update
The raw WGS data from the ROSMAP, MSBB, and MayoRNAseq studies is now available in Synapse: syn15067647 . Please note that the data must be transferred to your own AWS account. Post a reply to this thread if you experience any issues, or have questions.
Created by Mette Peters Mette @krcochran and @mvcakir
RNAseq on the ROSMAP, MSBB, and MayoRNAseq can be found in the AD Knowledge Portal through the following studies
* [ROSMAP](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn3219045)
* [MSBB](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn3159438)
* [MayoRNAseq](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn5550404)
The MSBB, MayoRNAseq, and ~700 of the ROSMAP (dlpfc) data has also been processed using a common pipeline. That data can be found in the [RNAseq Harmonization Study](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn9702085)
WGS fastq files across the 3 cohorts are not available for direct download. Please [see here for instructions and data](https://www.synapse.org/#!Synapse:syn15067647/wiki/591142)
If you haven't already I encourage you to join the [AMP-AD_DataReleaseUpdates team](https://www.synapse.org/#!Team:3372003) for notifications through Synapse about data releases. Also, we publish a quarterly newsletter that may have content that interests you: https://news.adknowledgeportal.org/newsletter/
Are there any news @Mette regarding reaching to raw BAMs? We managed to get the new AMP-AD knowledge portal access. I'm really confused and I do not understand what the problem is frankly.
edit - OK I could get my hands on them. Thanks anyway :)
Edit2- Actually I realized I still cannot get them, for rnaseq they are available, but for genome they are only available in vcf. Is there any way I can get the raw reads from the WGS of ROSMAP study? @Mette I'm looking for both WGS and rnaseq. Thanks a lot for the quick reply. @Mette I'm looking for RNAseq data @krcochran and @mvcakir are you looking for WGS or RNAseq data? Dear Mette,
is AWS the only way or getting hands on bam files of ROSMAP? Is it not allowed to download bam files?
Thanks a lot.
Volkan Hello,
I'm trying to get access to the MSBB raw FASTQ files. I believe I have submitted and accepted the DUC for ROSMAP and the AMP-AD. In a previous discussion post I found a link (https://www.synapse.org/#!Synapse:syn8612096) that contains all the Mayo RNAseq raw FASTQ data and was wondering if there were a similar folder containing the MSBB raw FASTQ data. I'm a bit of a novice when it comes to the AWS cloud. Is this available? Or is the only way to download the MSBB FASTQ data through the cloud?
If it is only through the AWS cloud, how would I go about downloading it?
Thank you Hello @liucy the fastq and bam files are available, but not as direct download from the Synapse S3. Please see here: https://www.synapse.org/#!Synapse:syn15067647/wiki/591142. Let us know if you have questions @Mette I am also searching for BAM/FASTQ data for ROSMAP WGS data. Only found its VCF files. @eteleeb, please check [access requirements here](https://www.synapse.org/#!AccessRequirements:ID=syn3191087&TYPE=ENTITY) to see if there is anything missing. There is an agreement to acknowledge the data contributor in publications that also needs to be clicked on and is often missed. Hi,
We have submitted the signed DUC document (Dr. Oscar Harari , Washington University in St. Louis) for accessing AMP-AD Kowledge Portal and we received the approval email. However, I am still not able to download raw Fastq files for ROSMAP gene expression. I also did the certified quiz and accept all terms and conditions but no luck so far. Is there additional requirements I should have .
Thank you. @jojikt follow the instructions to the [DUC here](https://adknowledgeportal.synapse.org/#/DataAccess/DataUseCertificates)
Se the ROSMAP study in the [AMP-AD portal](https://adknowledgeportal.synapse.org/#/Explore/Studies?Study=syn3219045). Note the study metadata files (clinical, biospecimen, scRNAseq) and the link to all scRNAseq under study data. That batch of data does not include the scRNAseq from the Mathy's et al., paper. See 'related studies' for that Hi Please let me know the procedure to download ScRNA-seq of ROSMAP raw data set and how to do Data Use Certification (DUC) Agreement 1. 102 TB
2. GRCh37
3. We may consider this for future releases
4. See the link in the documentation to metadata and methods: https://www.synapse.org/#!Synapse:syn15067647/wiki/591142
A few questions about the ROSMAP WGS bam files....
1. How much storage is required to store a complete set of the bam files?
2. Are they aligned to GRCh37 or GRCh38?
3. CRAMs require much less storage(20% of bams). Could CRAMs be made available in addition to the bams to minimize the storage requirements?
4. Is there some documentation on the pipeline used to create the bams? @r.alalwany and others that have requested access to the ROSMAP, MSBB, and Mayo raw WGS data, it is now available here: syn15067647. Please follow the instructions for transferring the data to your own AWS account and let us know if you run into any issues. @Mette
Hi, could I please get access to the raw data from the ROSMAP study?
(I have a signed/approved DUC from RADC) Hi,
I would like to download the BAM files please, we should have the access sorted for ROSMAP and this is what I would please need (PI: Aviv Regev)
I am also like haklein above wondering where to find information on the tissue source for individual samples ie brain or blood?
Thanks ! Hi,
I would like to download the BAM files please, we should have the access sorted for ROSMAP and this is what I would please need (PI: Aviv Regev)
I am also like haklein above wondering where to find information on the tissue source for individual samples ie brain or blood?
Thanks ! Hi Mette,
I would like to transfer the WGS bam files (MSBB and Mayo) to our AWS account. Who do I have to contact or is there documentation somewhere?
I am also wondering whether there is information about the tissue source (brain region or blood) used for DNA extraction?
Thanks!
Hans
@mrhll - We are in the process of preparing the data for distribution through Synapse (it was previously distributed through MSSM), but because of the large size, data transfer from Synapse will be limited to transfer within the AWS infrastructure. You will be able to transfer the data for free from Synapse to your AWS account, but any subsequent analysis, long-term data storage, or data transfer to local servers will incur AWS charges. Instructions about this will be posted soon. We will post an update when it is in place Hi,
I want to access the raw data.
Thanks,
Caroline.
Hi @Karen_Crawford - These datasets are controlled access. The first step is to agree to the terms and submit the ROSMAP and AMP-AD portal DUCS (covers the MSBB and Mayo sequencing data). See instructions here: https://ampadportal.org/#/DataAccess/DataUseCertificates
Going forward, the raw data will be distributed through Synapse (it was previously distributed through MSSM), but because of the large size, data transfer from Synapse will be limited to transfer within the AWS infrastructure. You will be able to transfer the data for free from Synapse to your AWS account, but any subsequent analysis, long-term data storage, or data transfer to local servers will incur AWS charges. Instructions about this will be posted soon.
The vcf's are currently available for download with no cost to the end user. See information here: https://www.synapse.org/#!Synapse:syn10901600 Hello,
I would like to access the ROSMAP, MSBB, and MayoRNAseq raw WGS data. How can I get access please?
Thanks Hi Mette,
We've got the access permission to the Mayo and MSBB WGS data. Could you please send the confirmation to data provider?
Thanks,
Yun @sterding - We have confirmed that you have the required DUCs. I will put you in touch with the group that will transfer you the raw WGS yes, I can download files (incl. the RNAseq bam files). Just no idea where to download the **raw** WGS files. Hi @sterding - are you able to download files? For, example: syn11384608 for MSBB and syn11384589 for ROSMAP HI Mette,
Could you please confirm if I have the needed DUC in place for ROSMAP/MSBB raw WGS data? When I clicked the https://www.synapse.org/#!AccessRequirements:ID=syn10901600&TYPE=ENTITY, it says "Your data access request has been approved" (a green button).
Thanks a lot,
-Xianjun Regarding ROSMAP data, they said
"The terms for data access cannot be modified'
https://www.synapse.org/#!AccessRequirements:ID=syn10901595&TYPE=ENTITY
Did ROSMAP have a contact email? @gibbs, @yzhu5 - we have confirmed that you have the needed DUC in place. I will put you in touch with the data provider Hi Mette,
Just wanted to follow up on my request on 12/05/18 for access to the ROSMAP raw WGS data. Thanks!
Yun Hi Mette,
I would like to access the ROSMAP raw WGS data. The DUC is on file. Could you please let me know how to get the raw data?
Thanks,
Yun I have a ROSMAP DUC in place and would like access to the ROSMAP WGS fastqs, thanks. Thank you Mette!
@mparanjpe96 , @alicelee - we have verified that you have the correct DUCs in place. I will put you in touch with the team that is distributing the data Hi Mette,
When I login with my username mparanjpe96 and click on the DUC for MSBB/MayoRNAseq https://www.synapse.org/#!AccessRequirements:ID=syn10901595&TYPE=ENTITY and ROSMAP https://www.synapse.org/#!AccessRequirements:ID=syn10901600&TYPE=ENTITY both pages say my request has been approved. I also got an email from Synapse saying that both requests were approved.
I submitted the DUC using the username mparanjpe96. My Synapase email: mparanjpe96@synapse.org
The name should be Manish Paranjpe @mparanjpe96 - Access to these data requires that you have submitted data specific Data Use Certificates. We do not see DUCs under your name for these studies. Were they submitted under a different name? If you have not submitted them let me know and I will send you directions Hi Mette,
Just wanted to follow up on my request on 11/15/18 for access to the ROSMAP, MSBB, and MayoRNAseq raw WGS data. Thanks!
Manish Hi Mette,
I would like to access the ROSMAP, MSBB, and MayoRNAseq raw WGS data. I have already completed the DUC for these studies. Is it possible to access them? Thanks!
Manish Paranjpe Hi Mette, I'd like to access the raw MSSB and Mayo WGS bam files. I had submitted DUC for MSSB and Mayo data access and it got approved. Thank you. Hello,
Yes, I need access to only raw MSBB WGS Data.
Thank you,
Kory Johnson
Hi @johnsonko - The raw data is available directly from Mount Sinai until the end of the year. We are in the process of transferring the data into an S3 that will be linked through Synapse. We will need to first verify that you have the required DUC(s) in place. Can you confirm that it's only the MSBB data you want Hello,
Wanted to ask please if you can confirm that access to the MSBB WGS raw data files is not yet possible? Or, am I incorrect and files are available for download?
Look forward to firm word one way or the other.
Thank you in advance.
Best,
Kory Johnson (synapse user id = johnsonko) Yes, the request is only for the ROSMAP data not for the MSBB and Mayo data. Thank you. Hi @alicelee - can you please confirm if this is only for the ROSMAP, and not the MSBB and Mayo WGS Hi Mette, We'd like to access ROSMAP WGS bam files?already have the approved DUC. Many thanks, Alice Hi Yes, at this time I need only the WGS-Seq data files for the MSBB samples. Thank you. Kory @vikaspeddu - we have delayed data access through S3 until early next year. I will put you in touch with the group that can facilitate direct transfer to you. Can you please confirm that you want access to all 3 datasets (ie, ROSMAP, Mayo, MSBB) @jhsul - I will put you in contact with the group doing the data transfer @johnsonko - can you please confirm that it is only the MSBB study you want the raw data from @mparanjpe96 - we do not see DUCs under your name for these studies. Were they submitted under a different name? Hi Mette,
I would like to access the ROSMAP, MSBB, and MayoRNAseq raw WGS data. I have already completed the DUC for these studies. Is it possible to access them? Thanks!
Manish Paranjpe Hello,
I just received an email stating my access request to the MSBB WGS raw data files was approved. Can you please provide details on where I can go to download the data as well as where the companion meta table can be downloaded?
Thank you in advance.
Best,
Kory Johnson (synapse user id = johnsonko)
Hi @jhsul
I just posted this to the top of the thread "The WGS is being moved to Amazon S3, and is currently not available. An update will be provided here once a process for data access has been put in place". Hello Mette,
I have permission to the ROSMAP, MSBB, and MayoRNAseq WGS data. Could I have access to the raw WGS data for all three (BAM files)?
Thank you,
Jae-Hoon You can access the MSBB fastq as part of the RNAseq reprocessing project: https://www.synapse.org/#!Synapse:syn9734203. See here for how they were generated: https://www.synapse.org/#!Synapse:syn9702085
There is at this point no plan to release the WES raw files Hi Mette,
Thanks for the quick reply! Is it the same story for fastq files for the MSBB exome and rnaseq reads?
Thanks,
Vikas Hi Vikas, we are in the process of moving the WGS data to AWS. They will be unavailable until that has been completed. I will post an announcement and instructions once the move has been completed.
Best,
Mette Hi,
I'd like to gain access to the raw read/fastq files for the WGS data, and the RNAseq data if possible
Please let me know how to best go about this. Hi Mette,
We've got the access permission to the Mayo and MSBB WGS data, where can I get the vcf with individual genotype information? Many thanks.
Hi Mette,
can I or my PI (Panos Roussos) get access to raw BAM/FASTQ? Thank you!
Id like to access RAW BAM/FASTQ files. The compliance team has reviewed and approved our requests. Thank you Hi Mette,
We have approval for just ROSMAP cohort , and so would like to get access the raw WGS data for ROSMAP.
Thanks
Sharvari Hi Mette, we received approval for the ROSMAP data, can you please let us know how to download the raw fastq data. Thank you in advance! Hi Mette,
We only need the ROSMAP raw WGS as we were previously granted access to the Mayo and MSBB data.
Thanks,
Sam Hi @sls18 - same question for you - do you want access to only the ROSMAP WGS, or the full set (ie the MSBB and Mayo data as well). If the later also, you will need to have the [ M2OVE-AD Consortium and the AMP-AD WGS Initiative DUC](https://www.synapse.org/#!AccessRequirements:ID=syn8272982&TYPE=ENTITY) as well @sgujja - do you want access to only the ROSMAP WGS, or the full set (ie the MSBB and Mayo data as well). If the later also, you will need to have the [ M2OVE-AD Consortium and the AMP-AD WGS Initiative DUC](https://www.synapse.org/#!AccessRequirements:ID=syn8272982&TYPE=ENTITY) as well Hi,
We have approval to access data for the ROSMAP study, and would like to get access to the raw WGS data as well. Could you please get me in touch with the data transfer group.
Thanks
Sharvari Hi Mette,
We have submitted a request to access the ROSMAP WGS data, once approved we would also like to have access to the Raw Data as well. Thank you!
Hi Mette,
Am I able to get access to the raw .fastq files for the RNA sequencing in the MayoRNAseq project (syn3163039 and syn5049298)?
Thanks,
Sam HI Mette,
Thanks for the update. I am awaiting for the group to contact me. Will they be sending me emails or contacting me here?
Rui Hi @ruichang we will let the group that is responsible for raw data transfer know. They will be contacting you. @Mette Could you give me the access to WGS bam/fastq files since my DUC has been approved?
@sxchen - you will need to add your name to the existing DUC and submit it
For ROSMAP, see how upload the DUC here: https://www.synapse.org/#!AccessRequirements:ID=syn3219045&TYPE=ENTITY
For the MSBB and MayoRNAseq WGS (the M2OVE-AD Consortium and the AMP-AD WGS Initiative DUC), see how to upload the DUC here: https://www.synapse.org/#!AccessRequirements:ID=syn10901600&TYPE=ENTITY If I just joined a lab that has a DUC in place, can I get added to access synapse files? What is the protocol in this situation? Thanks, Mette! We should have all the DUC paperwork in order -- appreciate your help! Also thanks for the quick reply! Hi @ghostmachina, we will first need to verify that you have the needed DUCs in place. Once that is done, we will put the data transfer group in touch with you Hi Mette, I also would like to request a WGS raw data transfer for all studies (MSBB, Mayo and ROSMAP). Can you put me into contact with the group? Thanks! Hi Samantha,
We have verified that you have the correct DUC in place, and let the group that is responsible for raw data transfer know. They will be contacting you.
Best,
Mette Hi Mette, we received approval for the MSBB and Mayo data downloads, please let me know how to obtain the raw data. Thank you! Hi Mette, for now we only want the MSBB and Mayo data. We will request the ROSMAP data as well, but we have not yet submitted the DUC for ROSMAP. Thank you! Hi Samantha, can you clarify if you only want access to MSBB and Mayo, and not ROSMAP We have submitted a request to access the MSBB and MayoRNAseq WGS data, we would also like to have access to the Raw Data as well. Thank you! Thank you for the clarification !! Hi Rami, access to the MSBB and Mayo WGS requires that you have an additional DUC in place. This is a DUC that covers the WGS from these 2 studies and all current and upcoming human data generated through the M2OVE-AD funding mechanism. The ROSMAP WGS was not put under this DUC, because use of any ROSMAP data requires terms specified by Rush. I know this is a bit confusing, and we will be working with our data providers to try to simplify the process.
Follow the instructions here: https://www.synapse.org/#!AccessRequirements:ID=syn10901600&TYPE=ENTITY
Let us know if you have additional questions about the process We already have signed the DUC for the ROSMAP data and we have a data statement posted on the AMPAD portal (Dr. Joshua Shulman, Baylor College of Medicine), but I can't access the MSBB and Mayo WGS data? also can we have access to the raw data ? thank you. @trajnp and @tswingo. We verified that you both have the required DUCs and let @ew3388 know that you have been approved Where are the fastq files? Following those links indicates my request for access was approved. Thanks. How do we get access to the RAW BAM/FASTQ files? Thanks!
Drop files to upload
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