Forum
Problem in ICGC Data Portal
For 3 days now, when I enter the ICGC Data Portal I get the error:
"This site can’t be reached"
Anyone know what the problem is?
Is there another way to enter the portal?
Thanks
Posted by Or Y over 1 year ago
Data upload
How can I upload my private data to the CGC?
Posted by Darko Kostadinovic over 2 years ago
What is the paper.iCluster.Group parameter?
LUAD clinical data has a parameter paper_iCluster.Group. What does it stand for, I can't find the definition anywhere
Posted by Bernardo Ramos over 2 years ago
How do I disable email notifications after job completion?
How do I disable email notifications after job completion?
Posted by Graham Erwin about 3 years ago
TCGA BAM file size inconsistency with GDC?
Hi,
I'm doing somatic mutation calling of a TCGA patient TCGA-AR-A1AO and am using the BAM file in databrower. I'm using the BAM files
TCGA-AR-A1AO-10A-01D-A12Q-09_IlluminaGA-DNASeq_exome_gdc_realn.bam
uuid:30f1d9e3-e6a5-44b6-846c-1497806d301c
size: 27.03GB
TCGA-AR-A1AO-01A-01D-A12Q-09_IlluminaGA-DNASeq_exome_gdc_realn.bam
uuid: 33eeb804-ca8b-491e-8221-a285743be692
size: 25.53GB
However, on GDC portal, the files are 29.02GB and 27.41GB respectively. I wonder if those files are really up to date as the file sizes are different and my somatic mutation calling result using Varscan2 is missing variants comparing to GDC results(Under same parameters and inputs.) It is just confusing so I am troubleshooting right now. Woule you please help me on this? Thanks!
Best,
Stella
Posted by Yiyun Rao over 3 years ago
Modify Read-only file in terminal
Hi!
I am analyzing the TCGA MAF files using terminal in Data cruncher. Some MAF files are .gz format and I have to unzip them. But it's a read-only file system. Would you please help find a solution? Thank you!
Best,
Yiyun
Posted by Yiyun Rao over 3 years ago
Varscan2 work flow from BAM producing too few somatic mutation calls?
Hi!
I am recently using the Varscan2 workflow from BAM to do somatic mutation calling of TCGA GRch38 BAM files. However, the output high confidence vcf files is only a few kb large. One of the patient I was looking, TCGA-AR-A1AO has around 6000 mutations called in the MuTect vcf but only have 300 mutations in my output.
I didn't change any parameters. I wonder if it's the problem of input files but I was just using the tumor-normal bam in TCGA.
Posted by Stella Lee over 3 years ago
Centrifuge custom index
I've used centrifuge locally to generate an index based on the GenBank database. The output of this operation is 4 files with the *.cf extension. once I try to use them to run a centrifuge run on the cloud it asks for the index in tar.gz format. what does it mean? Then I'm trying to run the indexing on the cloud but I've found only a pipe to use RefSeq but not GenBank and in general, I would like to do it locally to have more freedom. now I'm running this script on the cloud: "Reference Index Creation " to create an index based on RefSeq and have the output in tar format but it is not exactly what I want to do. there is a way to have the index in tar format with centrifuge locally or to use genbank database in this cloud app to generate the index?
Posted by Rosario Brancaccio over 3 years ago
How to download many files from a project to a volume?
Greetings. I was wondering if you could help me. I have a number of files in a project that I am on that I would like to copy to an Amazon S3 bucket. I have mounted the bucket on a volume. However, it is not clear how to copy the files to the bucket. While https://docs.cancergenomicscloud.org/docs/aws-cloud-storage-tutorial#move-file-from-project shows how to move a particular file, I would like to move many files. Is this something that can be done via the Cancer Genomics Cloud GUI/web interface, or is there is some link showing me how it can be done? Many thanks!
Posted by Toshiro K. Ohsumi over 3 years ago
STAR genome generate (2.7.0e) error
Hi, I'm using STAR genome generate and STAR from public apps (both 2.7.0e) to align a human RNA-seq data (uploaded privately) and I'm using GRCh38.primary_assembly.genome.fa and gencode.v32.annotation.gtf as the reference genome and gene annotation file for genome indices generation. I keep getting this error:
Command mkdir genomeDir && STAR --runMode genomeGenerate --genomeDir ./genomeDir --runThreadN 20 --genomeChrBinNbits 16 --limitGenomeGenerateRAM 60000000000 --genomeFastaFiles /sbgenomics/workspaces/2bc67190-cbb2-43ba-866b-ca9e77ce024a/tasks/a72a496a-3859-480c-8de1-31c0e332b50e/star_genome_generate_2_7_0e/GRCh38.primary_assembly.genome.fa --sjdbGTFfile /sbgenomics/workspaces/2bc67190-cbb2-43ba-866b-ca9e77ce024a/tasks/a72a496a-3859-480c-8de1-31c0e332b50e/star_genome_generate_2_7_0e/gencode.v32.annotation.gtf && tar -vcf GRCh38.primary_assembly.genome.gencode.v32.annotation.star-2.7.0e-index-archive.tar ./genomeDir && mv Log.out Log.out.log failed with exit code 137.
Can someone tell me how to solve this? Thank you!
Posted by Jillian Sieh over 3 years ago