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14 changes: 7 additions & 7 deletions docs/genomics-platform/faq/index.md
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Expand Up @@ -41,7 +41,7 @@ at St. Jude) or an external user. If you are a St. Jude Employee, please refer
to the dedicated [intranet
page](https://home.stjude.org/computational-biology/Pages/bioinformatics-self-service-cloud.aspx)
for instructions. If you are not a St. Jude Employee, please refer to our
[Create an Account](./accounts-and-billing.md#billing-setup) guide.
[Create an Account](../accounts-and-billing/#billing-setup) guide.

## Does St. Jude Cloud allow for-profit companies to access genomics data?

Expand All @@ -51,7 +51,7 @@ We do not allow for-profit companies to access any of our restricted access geno
## Why do I need to sign the Data Access Agreement (DAA)?

The [data access
agreement](./requesting-data/glossary.md#data-access-agreement)
agreement](../requesting-data/glossary/#data-access-agreement)
serves many purposes. Ultimately, the terms included in the data access
agreement are in place to protect our patients. We take patient security very
seriously, and we require that requesters are committed to protecting that
Expand Down Expand Up @@ -80,19 +80,19 @@ You can download the latest version of the DAA

You can submit your Data Access Agreement in the drag and drop box on the [last
step of the data request
process](./requesting-data/data-request.md#requesting-data).
process](../requesting-data/making-a-data-request/#requesting-data).

## What if I did not fill out the Data Download Permission section of the original DAA, but now I want to download data?

This would be a change in terms from the original agreement, you would need to
fill out a new DAA (including the [Data Download Permission
section](./requesting-data/how-to-fill-out-DAA.md#the-data-access-agreement)
section](../requesting-data/how-to-fill-out-daa/#the-data-access-agreement)
for any data sets you want to download.

## What clinical information is available about samples in St. Jude Cloud?

You can view the basic clinical and phenotypic information we currently provide
[here](./requesting-data/about-our-data.md#metadata).
[here](../requesting-data/about-our-data/#metadata).

## Can I gain access to further clinical information than what is currently available?

Expand All @@ -117,11 +117,11 @@ storage cost without any benefit. Several tools exist that you can leverage to
revert BAM to FASTQ files — we recommend using Picard SamToFastq to revert BAM
files. You can efficiently revert BAMs to FASTQs in the cloud by wrapping the
conversion tool of your choice into a [Cloud
App](./analyzing-data/creating-a-cloud-app.md)
App](../analyzing-data/creating-a-cloud-app)

## How can I work with genomics data in the cloud?

You can view [this guide](./analyzing-data/creating-a-cloud-app.md) to learn how
You can view [this guide](../analyzing-data/creating-a-cloud-app) to learn how
create a cloud application.

## Why am I getting a connectivity error when connecting to DNAnexus API via SSH?
Expand Down
8 changes: 4 additions & 4 deletions docs/genomics-platform/managing-data/how-to-fill-out-extension/index.md
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Expand Up @@ -5,7 +5,7 @@ title: Filling Out The Extension Addendum

#Filling Out The Extension Addendum

The St. Jude Cloud [Data Access Agreement (DAA)](../requesting-data/glossary.md#data-access-agreement) is only valid for one year after the date it was approved. When your DAA is about to expire, you will get an automated email from notifications@stjude.cloud with the name of the DAA that is expiring and a link to the St. Jude Cloud Extension Addendum.
The St. Jude Cloud [Data Access Agreement (DAA)](../../requesting-data/glossary/#data-access-agreement) is only valid for one year after the date it was approved. When your DAA is about to expire, you will get an automated email from notifications@stjude.cloud with the name of the DAA that is expiring and a link to the St. Jude Cloud Extension Addendum.

In order to extend your DAA, you must fill out an Extension Addendum. The Extension Addendum will extend the previous agreement for an additional year. Please note that if you do not fill out an Extension Addendum, you will be expected to delete all copies of the data subject to the expiring agreement.

Expand All @@ -22,7 +22,7 @@ Follow the steps below to ensure that you have accurately filled out all section


2. **Page 2**
* Check exactly the datasets that you were granted access to by the terms of the original DAA. *The datasets checked on the original DAA and any extensions must match.* If you would like to apply for access to additional datasets, please [make a new data request](../requesting-data/data-request.md) for the additional dataset(s).
* Check exactly the datasets that you were granted access to by the terms of the original DAA. *The datasets checked on the original DAA and any extensions must match.* If you would like to apply for access to additional datasets, please [make a new data request](../../requesting-data/making-a-data-request) for the additional dataset(s).

* The Principal Investigator (PI) or faculty level supervisor on the project must sign and date the extension. *The PI who signed the original DAA must match the PI signing any extensions.*

Expand All @@ -46,5 +46,5 @@ Once you have finished filling out the Extension Addendum, you may upload the co

## Similar Topics

[About our Decision Process & Terminology](../requesting-data/glossary.md)
[Filling Out a Data Access Agreement](../requesting-data/how-to-fill-out-DAA.md)
[About our Decision Process & Terminology](../../requesting-data/glossary)
[Filling Out a Data Access Agreement](../../requesting-data/how-to-fill-out-daa)
16 changes: 8 additions & 8 deletions docs/genomics-platform/managing-data/working-with-our-data/index.md
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Expand Up @@ -3,12 +3,12 @@ title: Working With Our Data
---


In this overview, we will explain how to manage your data request(s) from St. Jude Cloud's genomics platform [My Dashboard page](https://platform.stjude.cloud/dashboard) and how to access and manage your data (once it has been vended to you) from within a DNAnexus project. The [DNAnexus](https://www.dnanexus.com/) genomic ecosystem is the backbone for the computation and storage in St. Jude Cloud. This means that each data request in St. Jude Cloud corresponds to a project in DNAnexus. If you'd like, you can read an introduction to the DNAnexus ecosystem [here](https://documentation.dnanexus.com/). If you haven't already, follow [this guide](../requesting-data/data-request.md) to request access to St. Jude data in this secure cloud ecosystem.
In this overview, we will explain how to manage your data request(s) from St. Jude Cloud's genomics platform [My Dashboard page](https://platform.stjude.cloud/dashboard) and how to access and manage your data (once it has been vended to you) from within a DNAnexus project. The [DNAnexus](https://www.dnanexus.com/) genomic ecosystem is the backbone for the computation and storage in St. Jude Cloud. This means that each data request in St. Jude Cloud corresponds to a project in DNAnexus. If you'd like, you can read an introduction to the DNAnexus ecosystem [here](https://documentation.dnanexus.com/). If you haven't already, follow [this guide](../../requesting-data/making-a-data-request) to request access to St. Jude data in this secure cloud ecosystem.


## Managing Your Data Requests

Below is a snapshot of the [My Dashboard](https://platform.stjude.cloud/dashboard) on our Genomcis Platform. From this page you can check the status of your data request, complete an [EDAA](../requesting-data/how-to-fill-out-DAA.md#the-electronic-data-access-agreement-process) draft, upload a revised [DAA](../requesting-data/how-to-fill-out-DAA.md) or an [Extension Addendum](how-to-fill-out-Extension.md), or link to your DNAnexus project folder for a specific data request.
Below is a snapshot of the [My Dashboard](https://platform.stjude.cloud/dashboard) on our Genomcis Platform. From this page you can check the status of your data request, complete an [EDAA](../../requesting-data/how-to-fill-out-daa/#the-electronic-data-access-agreement-process) draft, upload a revised [DAA](../../requesting-data/how-to-fill-out-daa) or an [Extension Addendum](../how-to-fill-out-extension), or link to your DNAnexus project folder for a specific data request.

![](./docs-manage-data-page-labelled-tagged.png)

Expand Down Expand Up @@ -38,18 +38,18 @@ project_space/
└── SAMPLE_INFO.txt
```

The `SAMPLE_INFO.txt` file provides all the [metadata](../requesting-data/about-our-data.md#metadata) associated with the request, and the restricted folder contains all the data for which you were approved separated by file type.
The `SAMPLE_INFO.txt` file provides all the [metadata](../../requesting-data/about-our-data/#metadata) associated with the request, and the restricted folder contains all the data for which you were approved separated by file type.


## Using Your Data

There are two primary ways you can interact with data vended to you in St. Jude Cloud:

* **Cloud access**. You can choose to work with the data in DNAnexus' genomics cloud ecosystem. This is our suggested method of interaction, as you can avoid downloading the data to your local servers (which both takes time and is error prone). If you choose to leverage this approach, you can either wrap your own analysis pipeline as a cloud app (see [our guide](../analyzing-data/creating-a-cloud-app.md)) or leverage any of DNAnexus' publicly available apps (see [DNAnexus' guide](https://documentation.dnanexus.com/user/running-apps-and-workflows).
* **Download the data** (*not suggested*). The second way to interact with data vended to you in St. Jude Cloud is by downloading the data to your local servers. If you wish to do this, you can download the data on the command line (see [our guide](../analyzing-data/command-line.md)). **Note that you must have indicated you wish to download the data in your [data access agreement](../requesting-data/how-to-fill-out-DAA.md#the-data-access-agreement).**
* **Cloud access**. You can choose to work with the data in DNAnexus' genomics cloud ecosystem. This is our suggested method of interaction, as you can avoid downloading the data to your local servers (which both takes time and is error prone). If you choose to leverage this approach, you can either wrap your own analysis pipeline as a cloud app (see [our guide](../../analyzing-data/creating-a-cloud-app)) or leverage any of DNAnexus' publicly available apps (see [DNAnexus' guide](https://documentation.dnanexus.com/user/running-apps-and-workflows)).
* **Download the data** (*not suggested*). The second way to interact with data vended to you in St. Jude Cloud is by downloading the data to your local servers. If you wish to do this, you can download the data on the command line (see [our guide](../../analyzing-data/command-line)). **Note that you must have indicated you wish to download the data in your [data access agreement](../../requesting-data/how-to-fill-out-daa/#the-data-access-agreement).**

## Similar Topics

[About our Data](../requesting-data/about-our-data.md)
[Making a Data Request](../requesting-data/data-request.md)
[Upload/Download Data (local)](../managing-data/upload-local.md)
[About our Data](../../requesting-data/about-our-data)
[Making a Data Request](../../requesting-data/making-a-data-request)
[Upload/Download Data (local)](../upload-local)
6 changes: 3 additions & 3 deletions docs/genomics-platform/requesting-data/about-our-data/index.md
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Expand Up @@ -120,7 +120,7 @@ RNA-Seq BAM files are mapped to HG38. For alignment, `STAR` v2.7.1a 2-pass mappi
```

## Data Access Units
We currently have the five [Data Access Units (DAU)](../requesting-data/glossary.md#data-access-unit) listed below. [Basic clinical data](#clinical-and-phenotypic-information) is available for relevant subjects in each DAU. Click on the DAU's abbreviation below to navigate directly to that DAU's [Study page](../../../guides/studies/index.md) for more detailed information.
We currently have the five [Data Access Units (DAU)](../glossary/#data-access-unit) listed below. [Basic clinical data](#clinical-and-phenotypic-information) is available for relevant subjects in each DAU. Click on the DAU's abbreviation below to navigate directly to that DAU's [Study page](../../studies/) for more detailed information.

### Pediatric Cancer Genome Project (PCGP)
**[PCGP](https://stjude.cloud/studies/pediatric-cancer-genome-project) is a paired-tumor normal dataset focused on discovering the genetic origins of pediatric cancer.**
Expand Down Expand Up @@ -172,14 +172,14 @@ Each data request includes a text file called `SAMPLE_INFO.txt` that provides a
| sample_name | A unique sample identifier assigned internally at St. Jude. |
| sample_type | One of Autopsy, Cell line, Diagnosis, Germline, Metastasis, Relapse, or Xenograft. |
| sequencing_type | Whether the file was generated from Whole Genome (WGS), Whole Exome (WES), or RNA-Seq. |
| file_type | One of the [file types](../../guides/data/types-of-data) available in St. Jude Cloud. |
| file_type | One of the file types available in St. Jude Cloud. |
| description | Optional field that may contain additional file information. |
| sj_diseases | If your data request was process after August 18, 2020, the field should be interpreted as the harmonized St. Jude Cloud diagnosis based on the best available information (data provided by the lab or PI and followup by scientists on the St. Jude Cloud team). If your data request was processed before August 18, 2020, this field should be interpreted as the disease identifier assigned at the time of genomic sequencing (keyly, the diagnosis known at the time of genomic testing may not be the best available information). **If your data request was processed after August 18, 2020 and you'd like to use the most up to date, harmonized diagnosis**, we recommend using `sj_diseases` when including diagnosis in your analysis. If your data request was made before this time *or* if you wish to use the values exactly as provided by the lab or PI, we recommend using the lab-provided value in `attr_diagnosis`. |
| sj_datasets | If present, the datasets in the data browser which this file is associated with. |
| sj_pmid_accessions | If the file was associated with a paper, the related [Pubmed][pubmed] accession number. |
| sj_ega_accessions | If the file was associated with a paper, the related [EGA][ega] accession number. |
| sj_dataset_accession | If present, the permanent accession number assigned in St. Jude Cloud. |
| sj_embargo_date | The [embargo date](glossary.md#embargo-date), which specifies the first date which the files can be used in a publication. |
| sj_embargo_date | The [embargo date](../glossary/#embargo-date), which specifies the first date which the files can be used in a publication. |

### Clinical and Phenotypic Information

Expand Down

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