X chromosome CNV analysis

Hello,

I am doing targeted DNA sequencing on the X chromosome and I would like to know if it is possible to analyse this sequencing data to detect Copy Number Variants.

Thank you

next-gen

• 1,860 views • link

updated 9.4 years ago by IP

• written 9.4 years ago by neks •

1 answer

CNVkit will do the thing, but be aware that for CNV analysis, sequencing of the whole chromosome will give you more reliable results.

• 0 views • link

written 9.4 years ago by IP

Thank you Iñigo. I will try it.

• 0 views • link

written 9.4 years ago by neks •

More posts like this

Calling structural variants from RNA-Seq data
written 3.6 years ago by Yasin Uzun •

Hi, I know that it is possible to call SNPs, indels using the GATK pipeline. However, I wonder whether it is possible to call large …
CNV calling, copy number calling, using ONLY Log2R values (with segmentation
written 4.6 years ago by jcn •

Hello all, I have two data files with the following columns: File 1, CGH_Probe_Table: Probe Name, Chromosome, Start, Stop, Feature Number, Log Ratio. File 2, …
CNVkit detected CNV number
written 5.3 years ago by enes •

Hi, I am newbie in CNVKit I want to analyse clinical exome panel sample in CNVkit to detect copy number variants. When I tried with …
Most common practice for targeted sequencing analysis tools?
written 9.4 years ago by lucakang •

Hi. I am currently doing targeted sequencing. We targeted 400genes with depth of 500. I just entered the field of bioinformatics and this is my …
detection of the copy number
written 10.9 years ago by Mohit •

Hello, How to detect the copy number of the chromosome in-silico? If I have data of Downs syndrome. How can I detect the copy number …
Forum: detection of the copy number!!!
written 10.9 years ago by Mohit •

Hello, How to detect the copy number of the chromosome in-silico? If I have data of Downs syndrome. How can I detect the copy number …
How is computed Mean Coverage from Illumina MiseqReporter ?
written 11.3 years ago by ZheFrench

We are doing targeted DNA Sequencing on Miseq sequencer. MiseqReporter let us export a file with Mean Coverage value for each targeted region. I' d …
Life Technologies MethylMiner sequencing on Solid 5500 - Analysis Pipelin
written 11.4 years ago by Maxime Lamontagne

Hello, I need to analyse methylation sequencing data done with the MethylMiner Enrichment Kit (no bisulfite conversion) and sequenced on Solid 5500. Does anyone know …
NGS DNA-seq analysis packages for mapping, calling cariants, annotation on R / bioconductor
written 11.4 years ago by houkto

Hi, I am looking for a complete DNA-seq analysis in R this including reads mapping, variants calling and annotation? So far I found RNA-seq and …
Copy number variation detection tools within exome sequencing
written 11.7 years ago by mangfu100

Hi. I would like to search copy number variation using exome sequence data. I have been using VarScan2 to detect copy number variations. However, I …