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the major command line tools (",{"type":430,"tag":676,"props":719,"children":721},{"className":720},[],[722],{"type":436,"value":723},"aria2c",{"type":436,"value":725},", ",{"type":430,"tag":676,"props":727,"children":729},{"className":728},[],[730],{"type":436,"value":731},"wget",{"type":436,"value":725},{"type":430,"tag":676,"props":734,"children":736},{"className":735},[],[737],{"type":436,"value":738},"curl",{"type":436,"value":740},", etc).\nNote that, if you choose to generate signed links to our data, it is your responsibility to ensure the links remain secure, including but not limited to the links remaining only known by yourself (so that others can not access the data in an authorized manner, as anyone can use them) and expiring as soon as possible (to minimize the amount of time the link is live).",{"type":430,"tag":439,"props":742,"children":743},{},[744],{"type":436,"value":745},"No commercial solution (such as Aspera) is available, nor are any custom transfer processes.",{"type":430,"tag":439,"props":747,"children":748},{},[749],{"type":436,"value":750},"We note here that downloading data at a large scale, no matter which tool is used, is an inherently unpredictable and unreliable process.\nThis is a key driving factor for why so many in the community (including ourselves with the St. Jude Cloud project) have adopted the model of bringing tools to the data in the cloud.\nWhile we allow users to download data from our platform, we recommend those having issues with downloading data analyze the data in the cloud or try downloading the data again at a later time with retries enabled.",{"type":430,"tag":431,"props":752,"children":754},{"id":753},"what-clinical-information-is-available-about-samples-in-st-jude-cloud",[755],{"type":436,"value":756},"What clinical information is available about samples in St. Jude Cloud?",{"type":430,"tag":439,"props":758,"children":759},{},[760,762,766],{"type":436,"value":761},"You can view the basic clinical and phenotypic information we currently provide ",{"type":430,"tag":478,"props":763,"children":764},{"href":61},[765],{"type":436,"value":630},{"type":436,"value":558},{"type":430,"tag":431,"props":768,"children":770},{"id":769},"can-i-gain-access-to-further-clinical-information-than-what-is-currently-available",[771],{"type":436,"value":772},"Can I gain access to further clinical information than what is currently available?",{"type":430,"tag":439,"props":774,"children":775},{},[776],{"type":436,"value":777},"We are working towards being able to provide additional clinical annotations such as treatment, outcome, and survival data in the future.\nUnfortunately, we do not offer it today and we do not have a timeline for when it will be available.",{"type":430,"tag":431,"props":779,"children":781},{"id":780},"can-i-get-a-copy-of-irb-consent-forms",[782],{"type":436,"value":783},"Can I get a copy of IRB consent forms?",{"type":430,"tag":439,"props":785,"children":786},{},[787],{"type":436,"value":788},"We do not provide individual consent forms or blank consent forms for any samples on St. Jude Cloud.\nWe have chosen to remain consistent with the requirements of the other major genomic data repositories in that (1) there is an internal vetting process by the St. Jude IRB to ensure samples may be shared with the research community, but (2) we do not share the informed consents with data requesters.",{"type":430,"tag":431,"props":790,"children":792},{"id":791},"can-i-request-fastq-files-on-st-jude-cloud",[793],{"type":436,"value":794},"Can I request FASTQ files on St. Jude Cloud?",{"type":430,"tag":439,"props":796,"children":797},{},[798,800,805],{"type":436,"value":799},"We do not store FASTQ files in St. Jude Cloud because it would double the storage cost without any benefit.\nSeveral tools exist that you can leverage to revert BAM to FASTQ files — we recommend using Picard SamToFastq to revert BAM files.\nYou can efficiently revert BAMs to FASTQs in the cloud by wrapping the conversion tool of your choice into a ",{"type":430,"tag":478,"props":801,"children":802},{"href":92},[803],{"type":436,"value":804},"Cloud App",{"type":436,"value":558},{"type":430,"tag":431,"props":807,"children":809},{"id":808},"how-can-i-work-with-genomics-data-in-the-cloud",[810],{"type":436,"value":811},"How can I work with genomics data in the cloud?",{"type":430,"tag":439,"props":813,"children":814},{},[815,817,822],{"type":436,"value":816},"You can view ",{"type":430,"tag":478,"props":818,"children":819},{"href":92},[820],{"type":436,"value":821},"this guide",{"type":436,"value":823}," to learn how create a cloud application.",{"type":430,"tag":431,"props":825,"children":827},{"id":826},"how-can-i-run-an-analysis-workflow-on-multiple-sample-files-at-the-same-time",[828],{"type":436,"value":829},"How can I run an analysis workflow on multiple sample files at the same time?",{"type":430,"tag":439,"props":831,"children":832},{},[833,835,839,841,847],{"type":436,"value":834},"The DNAnexus interface does have a batch tool available; however, it is in early testing, so we recommend using dx-toolkit on the command line as the most reliable and user friendly approach to batch and submit jobs.\nYou can find our documentation on how to install and get started with dx-toolkit ",{"type":430,"tag":478,"props":836,"children":837},{"href":86},[838],{"type":436,"value":630},{"type":436,"value":840},".\nYou may also refer to the sample script below that loops through all the BAM files in the ",{"type":430,"tag":676,"props":842,"children":844},{"className":843},[],[845],{"type":436,"value":846},"data",{"type":436,"value":848}," folder and submits a job using the BAM and matching index file.",{"type":430,"tag":850,"props":851,"children":855},"pre",{"className":852,"code":853,"language":854,"meta":424,"style":424},"language-bash shiki shiki-themes 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connectivity error, it may be that your firewall is too restrictive.\nAre you able to perform the command from an unrestricted network (like a home network)?\nIf yes, you can resolve this issue by asking your network administrator to whitelist connections to Azure US West.\nAll subnets (Region Name=\"uswest\") are provided ",{"type":430,"tag":478,"props":1103,"children":1106},{"href":1104,"rel":1105},"https://www.microsoft.com/en-us/download/details.aspx?id=41653",[482],[1107],{"type":436,"value":630},{"type":436,"value":558},{"type":430,"tag":431,"props":1110,"children":1112},{"id":1111},"how-can-i-delete-my-account",[1113],{"type":436,"value":1114},"How can I delete my account?",{"type":430,"tag":439,"props":1116,"children":1117},{},[1118,1120,1126],{"type":436,"value":1119},"Today, a St. Jude Cloud Genomics Platform account is simply a DNAnexus account.\nThus, of you'd like to delete your account, you'll need to email DNAnexus asking for it to be removed.\nYou can do so by contacting DNAnexus support at ",{"type":430,"tag":478,"props":1121,"children":1123},{"href":1122},"mailto:support@dnanexus.com",[1124],{"type":436,"value":1125},"support@dnanexus.com",{"type":436,"value":1127}," with the following email.",{"type":430,"tag":1129,"props":1130,"children":1133},"callout",{"color":1131,"icon":1132},"blue","i-heroicons-document-text-solid",[1134],{"type":430,"tag":439,"props":1135,"children":1136},{},[1137,1142,1146,1148,1151,1153,1156],{"type":430,"tag":453,"props":1138,"children":1139},{},[1140],{"type":436,"value":1141},"Subject: St. Jude Cloud account deletion",{"type":430,"tag":1143,"props":1144,"children":1145},"br",{},[],{"type":436,"value":1147},"\nHi DNAnexus,",{"type":430,"tag":1143,"props":1149,"children":1150},{},[],{"type":436,"value":1152},"\nWould you please assist me in deleting my St. Jude Cloud account? My username is _____.",{"type":430,"tag":1143,"props":1154,"children":1155},{},[],{"type":436,"value":1157},"\nThank you!",{"type":430,"tag":1159,"props":1160,"children":1161},"style",{},[1162],{"type":436,"value":1163},"html .light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html.light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html .default .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}html.dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}",{"title":424,"searchDepth":926,"depth":926,"links":1165},[1166,1167,1168,1169,1170,1171,1172,1173,1174,1175,1177,1178,1179,1180,1181,1182,1183,1184],{"id":433,"depth":926,"text":437},{"id":514,"depth":926,"text":517},{"id":542,"depth":926,"text":545},{"id":561,"depth":926,"text":564},{"id":580,"depth":926,"text":583},{"id":604,"depth":926,"text":607},{"id":615,"depth":926,"text":618},{"id":634,"depth":926,"text":637},{"id":652,"depth":926,"text":655},{"id":671,"depth":926,"text":1176},"Is there another mechanism for downloading the data besides using the dx command line tool?",{"id":753,"depth":926,"text":756},{"id":769,"depth":926,"text":772},{"id":780,"depth":926,"text":783},{"id":791,"depth":926,"text":794},{"id":808,"depth":926,"text":811},{"id":826,"depth":926,"text":829},{"id":1085,"depth":926,"text":1088},{"id":1111,"depth":926,"text":1114},"markdown","content:3.genomics-platform:1.getting-started:5.faq.md","content","3.genomics-platform/1.getting-started/5.faq.md","3.genomics-platform/1.getting-started/5.faq","md",[1192,1194],{"_path":43,"title":1193,"description":424},"Filling Out The Data Access Agreement",{"_path":48,"title":47,"description":1195},"About Our Decision Process and Terminology",1791243634068]