copy number of gene in the gap of segmentation file
I have a basic question for CNV segment output from Sequenza for WES data from paired tumor/normal samples.
There are always some gap between nearly segments, such as below example gap (17: 41165610-41368081) between these two samples on chr17.
17 30671151 41165609
17 41368082 41465708
How do we understand the copy number status in this segment gap, say chr17: 41165610-41368081? I checked the bam file and it seems we cannot simply consider this is CN=0 region for tumor. And it is really important because some key gene such as BRCA1 is in this gap region.
• 898 views
•
link
written
by
xiaoqiaoliu •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Analysing gene CNV from TCGA using TCGAbiolinks
written by Matt •
-
CNV calling using CN.MOPS
written by shivangi.agarwal800
-
CNVKit noisy scatter plot
written by tanbiswas6 •
-
Problem with CNVkit using samples with single-end sequenced WES
written by tangya1982 •
-
How to draw heatmap plot use cnv seg data called by gatk?
written by MatthewP
-
How to evaluate "control" genes in target sequencing data?
written by jinxinhao1988
-
Explications about call function of CNVkit
written by Hällyss
-
I need help with how to modify the sbdry parameter in DNAcopy
written by mikki •
-
R Copy Number Visualization/Summary Options
written by gaiusjaugustus
-
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
written by Chirag Nepal
