RDXplorer for GRCh38 · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

RDXplorer for GRCh38

I want to detect the copy number variation region via RDXplorer(http://rdxplorer.sourceforge.net/ ). However, the essential files, including gap, gc100, and gc10, just be provided for hg18 and hg19 in the latest version. If I want to use this tool for the NGS bam file with GRCh38, is any suggestion?

Thank you!

r next-gen sequencing

• 755 views • link

updated 6.6 years ago by GenoMax

• written 6.6 years ago by weiyuchung •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

BQSR using GATK BaseRecalibrator
written 3.6 years ago by Fatemeh Nabizadeh •

Hello everyone I'm trying to use the BQSR tool for my patient's aligned bam file (using bwa + GRCh38.p14 reference primary assembly), but I get …
liftOver VCF from hg38 to hg19
written 3.8 years ago by Isobel •

Hi, I am trying to lift the New York Genome Centre 1000 Genomes 30x on GRCh38 to GRCh37. As this file is a vcf I …
Tool: driveR - Prioritizing Cancer Driver Genes Using Genomics Data
written 5.7 years ago by egeulgen

Hello all, <img src="https://github.com/egeulgen/driveR/raw/master/inst/extdata/driveR_logo.png?raw=true" align="left" height=100/> I would like to introduce our group's new R package for driver gene prioritization: [driveR][1] (latest release is v0.2). …
Getting the db SNP VCF file for GRCh38.p13
written 6.2 years ago by nhaus •

Hello everybody, after searching a long time, I am still unable to find the db SNP VCF file with the coordinatse for GRCh38.p13. The latest …
How do I detect copy number variation from data generated by scNuc-seq?
written 6.6 years ago by wp.hou3 •

I have some cells sequenced by **scNuc-seq** technique including **.fastq**, **.bam** files and processed gene expression. I want to detect the **copy number variation(CNV)** for …
How to use multiple control in Control-FREEC for CNV analysis?
written 7.2 years ago by BioNoobie •

We have 15 control sample and 30 test sample and want to check copy number variation in test samples. The sequencing method used is ion-torrent …
Using hg38 assembly with hg19 exome capture data
written 7.5 years ago by jdm204 •

Hello all, I have some exome sequencing data which used an exome capture kit (http://emea.support.illumina.com/downloads/nextera-rapid-capture-exome-v1-2-product-files.html) from Illumina which is based on hg19 coordinates. I aligned …
Copy number variation detection
written 8.2 years ago by v27 •

i want to detect copy number variation among gene from whole genome sequencing data of bacteria. I have an idea how to detect the SNP/SNV's. …
CAF to population frequency
written 11.2 years ago by lyellooo •

Greetings. The story is that I want to use ContEst from the broad institute as one of my quality control tools for NGS data. However, …
Forum: Ensembl 74 Is Out
written 12.7 years ago by Emily

The latest Ensembl release is out. The new release includes: - Updated human GENCODE release 19 and mouse GENCODE release M2 gene sets including manual …