Hello,
I recently was approved for full access after submitting the data use agreement, how do I access the FASTQ files? I see on previous threads there is a data transfer group. Can they please help me with this?
Thank you very much,
Meaghan
Created by capa03 There is something going on with those files that appears to not have a resolution, yet. Please see [this thread](https://www.synapse.org/#!Synapse:syn2580853/discussion/threadId=6393) for more information. @jhogestyn @mzhang30 @MichaelDufault @E0423240 @bradfordelmer
Hi Nicole,
Thank you for your help. We were able to download the temporal cortex and cerebellum files. All of the tctx files aligned perfectly, but there were 27 cerebellum files that appear to be corrupt. We tried downloading them again but had the same problem. Here is a list of the files with this problem. Can you help us resolve this? Thank you very much
1000_CER
1029_CER
1085_CER
1103_CER
1104_CER
11271_CER
11285_CER
1129_CER
11300_CER
11456_CER
11460_CER
11491_CER
11497_CER
11505_CER
1214_CER
1302_CER
142_CER
1933_CER
1934_CER
1963_CER
6821_CER
6880_CER
751_CER
785_CER
791_CER
871_CER
991_CER
I apologize; I was thinking of MSBB.
The MayoRNAseq study is different from others in that the study data provided BAM files. However, these files have been reprocessed into fastq. Since the fastq are not the original files from the study, they are stored in a different area and can be [found here](https://www.synapse.org/#!Synapse:syn8612096). I am looking for the FASTQ files from the MayoRNAseq study-not the MSBB study. Can you show me the results of your query where you see FASTQ for MayoRNAseq? Thank you very much There are both BAM and fastq files in [this folder](https://www.synapse.org/#!Synapse:syn7416949).
How to download them depends on how you want to do so. We have ways to download via the website, R, or Python. Finding which files are fastq can be done in a variety of ways, as well. For example, [here is a query](https://www.synapse.org/#!Synapse:syn11346063/tables/query/eyJzcWwiOiJTRUxFQ1Qgc3R1ZHksIGRhdGFUeXBlLCBhc3NheSwgaWQgQVMgZmlsZV9pZCwgc3BlY2ltZW5JRCwgaW5kaXZpZHVhbElELCBkaWFnbm9zaXMsIHNleCwgY29uc29ydGl1bSBBUyBcIlByb2dyYW1cIiwgZ3JhbnQsIHNwZWNpZXMsIG9yZ2FuLCB0aXNzdWUsIGNlbGxUeXBlLCBmaWxlRm9ybWF0IEZST00gc3luMTEzNDYwNjMgV0hFUkUgKCAoIFwic3R1ZHlcIiA9ICdNU0JCJyApICkgQU5EIGZpbGVGb3JtYXQgPSAnZmFzdHEnIiwgImluY2x1ZGVFbnRpdHlFdGFnIjp0cnVlLCAiaXNDb25zaXN0ZW50Ijp0cnVlLCAib2Zmc2V0IjowLCAibGltaXQiOjI1fQ==) that has all the MSBB fastq files. There is a button for 'download options' that will allow you to add the files to a download list. When you choose to download from your download list, it will put them all in a zipped folder.
In the Synapse documentation, there are articles on [getting started with downloading](https://docs.synapse.org/articles/downloading_data.html) and [downloading in bulk](https://docs.synapse.org/articles/uploading_in_bulk.html), which go over some of the various ways to download data from Synapse. If there is a specific question you have, please let me know.
Thank you for your help. I do have access to download (the lock is green).
I only see count and BAM files. I did read the documentation to download files, so your saying with programming we can search, find, and download the FASTQ files even though I don't see them here?
Can you give me any more specific details on how to download? Thank you Provided that you have access to download the files (the access lock should be green on the file), you should be able to download the files. Please see the [Synapse documentation for getting started with downloading files](https://docs.synapse.org/articles/downloading_data.html). Hi @nicole.kauer,
I have accepted the terms of agreement. I am not sure if this was not done previously, but I have done it now. What are now the next steps to downloading the FASTQ files? Thank you so much for your help,
Meaghan Hi Meaghan,
There is also a click-wrap agreement that needs to be accepted. One way to check that this has been done is to look at the [access terms here](https://www.synapse.org/#!AccessRequirements:ID=syn5550404&TYPE=ENTITY). The button should be green and say that the terms of use have been accepted. Please let me know if this is not the issue.