Download 36k Valid Txt
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I downloaded expression data for TCGA-ESCA, there are 164 cases for this cancer, but there are 519 files with extension *.FPKM.txt.gz , *.FPKM-UQ.txt.gz & *.htseq.counts.gz. how to map with Tumor-ID/ Aliquot)id and make expression matrix (total tumor sample * all genes)?
1, manifest is formed by what you want to download. that means it is same with what you selected in the first stage, not same for all the data types. Finally, manifest is formed by what you selected. (add to cart in GDC website, means it was selected)
Musalulas-MacBook-Pro:~ sinkala$ /Users/sinkala/Downloads/gdc-client ; exit;usage: gdc-client [-h] [--version] {download,upload,interactive} ...gdc-client: error: too few argumentslogoutSaving session......copying shared history......saving history...truncating history files......completed.
I have also tried the alternate ways of installing the thing, but I have not been successful either.I have tried to download the data directly from the data portal; even that does not work for a file size less than 400mb - the server does not respond or something like that. :( :(
Please someone there.. could you helpe me.. I'm having trouble intalling gdc-client on ubuntu 14I downloaded the zip gdc and extracted after that, on the shell i wrote.. ./ gdc-client.. but nothing happen,,
I'm using gdc-client v1.2.0. I specifically sort my manifest file by patient id so I may download tumor-normal pair BAMs one after another. But in reality, BAMs were downloaded in some random order, which is not from the top to bottom of my sorted manifest file. Do other people have the same problem? Is there a way to fix it?
Hi,I have download GDC client tool to download files from GDC. As the download folder should contain data or zipped data and logs folder. My files are downloaded successfully. However, I see only few logs folder. For example for Bladder Urothelial carcinoma (BLCA) manifest files includes 433 UUID. But only 53 logs folder were found. Thus could you let me know is the download files are accurate?
The next code block downloads the 379 gene expression files specified in the query above. Using multiple processes to do the download very significantly speeds up the transfer in many cases. On a standard 1Gb connection, the following completes in about 30 seconds.
Thanks for the detailed view. One more clarification:When I try to download the WGS (whole genome sequencing data) for, say Breast cancer (TCGA-BRCA) from GDC Legacy, the second column of the manifest file for the same has some ids which are not sample IDs. What are those? e.g
A balenaOS image, by default, does not include any configuration informationto associate it with a fleet. When a customer downloads a provisioningimage from the Dashboard, balenaCloud injects the configuration for the specificfleet the image is being downloaded for. Similarly, the balena CLI allowsthe download of a balenaOS image for a device type (and specific version), butrequires that this image has a configuration added (usually via the use ofbalena os configure) before flashing to bootable media.
Whilst making the changes, the new configuration is written to the config.jsonfile, whilst we have a backup of the original (config.json.backup). Remember, should you need to change anything, always keep a copy of the original configurationso you can restore it before you exit the device. Check out the valid fields available to be configured on a balena device.
You can download the latest version of VERDI from -tool.org/ (see Figure 1-1). When you click on the link to download VERDI, you will be sent to the CMAS Model Download Center. To download and install VERDI, follow the instructions below, skipping step 2. Alternatively, you may also begin at the CMAS web site , and follow the instructions below:
Documentation is available in several locations, described below. Each location provides links to the available documentation for VERDI, which can be viewed in your web browser or downloaded and saved to your computer.
VERDI requires version 6 of the Java Standard Edition Runtime Environment (JRE). The JRETM 6 is provided as part of the VERDI release for Linux 32 bit and Windows. Instructions for how to download JRETM 6 and the additional third-party libraries for Linux 64 bit are provided in section 3.2.
For Linux platform with ia64 architecture, please find the installed jre or jdk library directory (ex. /usr/java/jre1.6.0_13/lib/ext or /usr/java/jdk1.6.0_11/jre/lib/ext) and copy all missing library files from $VERDI_HOME/jre1.6.0_13/lib/ext directory. If ia64 jre/jdk package is not installed, please go to java.sun.com download the install file and install the package. Then copy the missing library files from $VERDI_HOME/jre1.6.0_13/lib/ext directory.
After the variable names are added to the Formula Editor, click on the formula pane and use the cursor and the keyboard to type in the mathematical functions and operators where needed to create a valid formula (see Section 7.2 and Section 16). After the formula has been created in the Formula Editor, click the Add button, to place it in the list of formulas available in the Formula pane. 781b155fdc