Hi, I have downloaded two sets of fastq files from SRA database. PRJNA421846 (set1) contains Whole Exome Sequencing of tumor dataset form 96 patients (There …

I have a MAF file. It is mutational information available for TCGA Pan cancer dataset. [mc3.v0.2.8.PUBLIC.maf.gz][1] In this dataset I have two sets of barcode: …

Hi all, I was looking at the somatic mutation summary at GDC data portal. It seems there are 986 samples with matched tumor and normal …

I have recently got access to a dataset from the EGA database. I am having problems understanding the true meaning of Sample ID and Accession …

I want to use cnvkit to call copy number alterations (CNAs) from Whole Exome Sequencing data (WES) of a specific tumor. I have a set …

I am doing some annotation work. I am having two sets of genes. Set one is my reference database and set 2 is my query …

Hi there, I analyzed some publicly available exome-seq data, and do not have matched normal/germline. I identified somatic mutation (VCF format), by setting high filtering …

<p>I am attempting to call mutations of raw RNA-Seq of single prostate circulating tumor cells (<a href="http://science.sciencemag.org/content/349/6254/1351.abstract">paper</a>) without matching normals.</p> <p>From cursory research I found …

I am interested in calculating differential expression of genes for tumor vs. normal samples from RNASeq V2 level 3 datasets for TCGA (downloaded from UCSC …

Apologies if this has been asked - I assumed it would have been, but I can't seem to find it. I am trying to do …