Tag: ascat

Bioconductor – Bioconductor 3.18 Released

Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…

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sarek: Introduction

Introduction nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. The pipeline is built using…

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GISTIC from ASCAT

GISTIC from ASCAT 0 Hello everyone, I am trying to run GISTIC from ASCAT segments, however,i am running into the following error. 1935 segment overlaps detected I read somewhere that running bedtools merge would solve the problem, however I am not sure. Is anyone doing the same ? or adopting…

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The evolution of lung cancer and impact of subclonal selection in TRACERx

The TRACERx 421 cohort The TRACERx study (clinicaltrials.gov/ct2/show/NCT01888601) is a prospective observational cohort study that aims to transform our understanding of NSCLC, the design of which has been approved by an independent research ethics committee (13/LO/1546). Informed consent for entry into the TRACERx study was mandatory and obtained from every…

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PUREE: accurate pan-cancer tumor purity estimation from gene expression data

Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…

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Non-zero expression counts from deleted genes

Non-zero expression counts from deleted genes 0 Hi all, I’ve been looking at the RNA-seq data (STAR counts) for homozygously deleted genes (ASCAT copy number = 0) in TCGA and don’t understand what I’m seeing. I expected these genes to have zero or negligible TPMs, but actually the vast majority…

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Interpreting ASCAT CNV output

Interpreting ASCAT CNV output 1 Hello, I have two queries w.r.t ASCAT CNV data: How does one go about getting the total copy number for a given locus or chromosome from the ASCAT CNV.output results. What is the optimal way to filter the dataset to reduce the noise? I would…

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Need help with IGV interpretation

Need help with IGV interpretation 0 Hello all, I wanted to confirm if this is a true deletion? based on what i can observe, there is a drop in coverage, and it is also supported by the red line within the reads. However, i am concerned if 1 read is…

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