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Tag: Control-FREEC
Shallow whole genome sequencing approach to detect Homologous Recombination Deficiency in the PAOLA-1/ENGOT-OV25 phase-III trial
Polak P, Kim J, Braunstein LZ, Karlic R, Haradhavala NJ, Tiao G, et al. A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer. Nat Genet. 2017;49:1476–86. Article CAS PubMed PubMed Central Google Scholar Birkbak NJ, Wang ZC, Kim JY, Eklund AC, Li Q, Tian R, et…
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…
Segmentation fault error in CONTROL-FREEC
Hi, I am trying to run CONTROL-FREEC on diploid yeast samples to detect CNVs on a department cluster. The config file looks like this: [general] chrLenFile = yeast_chr.len ploidy = 2 window = 150000 #breakPointThreshold = -.002; #coefficientOfVariation = 0.062 chrFiles = /net/smith/vol1/home/student/FREEC-11.6b/data/test_sludge/yeast_files outputDir = /net/smith/vol1/home/student/FREEC-11.6b/data/test_sludge/output #degree=3 [sample] mateFile =…
Whole-genome doubling drives oncogenic loss of chromatin segregation
Cell culture hTERT-RPE-1 WT and hTERT RPE-1 TP53−/− (46, XX)27 cells were a gift from J. Korbel. The cells were grown in DMEM/F-12, GlutaMAX (10565018) supplemented with 10% FBS (Thermo Fisher Scientific, 10270106) and 1% antibiotic–antimycotic (Thermo Fisher Scientific, 15240062). CP-A (KR-42421) (47, XY) cells were purchased from the American Type…
Control-FREEC output
Control-FREEC output 0 Hello everybody, I’m using the tool Control-FREEC to evaluate the CNVs in my data, but I have some doubts about the _ratio.txt file in output. As far as I understood by both the paper and the documentation, this file should report the ratio (that, if I’m correct,…
iPSCs derived from infertile men carrying complex genetic abnormalities can generate primordial germ-like cells
Patients and controls The patient 1 was 38 years old and consulted for infertility after he and his partner had been trying to conceive for 2 years. The patient was the first child of unrelated parents, and he had four brothers and five sisters whose fertility status could not be determined…
CNV calling for wgs of S. pombe
CNV calling for wgs of S. pombe 0 Hi, Can anyone help to do CNV calling of WGS data of S.Pombe? I have 1 normal sample and 3 samples treated with a suppressor. I used Control-FREEC but did not get the right result. Can anyone help, how to do germline…
A genomic mutation spectrum of collecting duct carcinoma in the Chinese population
This article was originally published here BMC Med Genomics. 2022 Jan 3;15(1):1. doi: 10.1186/s12920-021-01143-2. ABSTRACT BACKGROUND: Renal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In…