CNVkit plotting tumor + healthy individuals

Hi, I was just wondering if there's any way to plot a heatmap of all affected/tumor samples + the normal samples together? I think the default is set to plot the affected samples only.. Thanks!

cnvkit software

• 1,706 views • link

updated 9.5 years ago by Eric T.

• written 10.2 years ago by bitpir

1 answer

Sorry I missed this. The heatmap command will plot any .cns or .cnr files you give it, so to show normal samples, give it the normal samples' .cns or .cnr files. If those don't exist yet (e.g. via batch), you can create them using the fix and segment commands.

• 0 views • link

written 9.5 years ago by Eric T.

More posts like this

Seurat PlotClusterTree together with heatmap of gene expression
written 3.3 years ago by miguellarrazlopezdenovales •

Hi Everyone, I am looking to plot a heatmap of gene expression together with hierarchical clustering of the samples. I can do each of them …
GATK Mutect2: Would a matched normal sample be redundant with a pool of normals that included the s…
written 3.6 years ago by Derrik •

I'm running Mutect2 on some paired tumor/normal samples. I've created the pool of normals and I'm about ready to run Mutect on the tumor samples, …
CNVkit: Dealing with noisy tumor samples
written 7.5 years ago by Fil •

Hi all, I have a question regarding CNV analysis (new CNVkit user). I am analyzing tumor samples from whole exome sequencing using CNVkit (v 0.9.3). …
getting feature annotations for all NCBI Refseq sequences
written 8.2 years ago by bitpir

Hi, I was wondering if there's a way to download all feature annotations (Gene; CDS; rRNA; tRNA; ncRNA; repeat_region) of all the Refseq sequences (ftp://ftp.ncbi.nih.gov/refseq/release/) …
Can anyone help me to confirm the number of matched tumor and normal samples in TCGA-BRCA?
written 8.5 years ago by Wen Wang •

Hi all, I was looking at the somatic mutation summary at GDC data portal. It seems there are 986 samples with matched tumor and normal …
software recommendations for identifying self from non-self dna sequences
written 9.1 years ago by bitpir

Hi there, I'm just wondering if there's a software out there that could help with identifying self from non-self dna sequences. I have the whole …
Two color microarray Heatmap
written 9.3 years ago by stomcan •

Hello Biostars I wish to plot a heatmap from a two color microarray data. The experiments used a common reference design and compared tumor samples …
fold enrichment calculation for exome sequencing
written 10.0 years ago by bitpir

Hi, I was wondering if there's a software available for calculating fold enrichment for exome sequencing? I see that USEQ's intersect region can calculate fold …
How many non-tumor samples needed for survival analysis?
written 10.1 years ago by jzhou •

Hi All, I've been working on my own survival analysis of PDAC, following the tutorial https://www.biostars.org/p/153013/, but after I separated the tumor and non-tumor samples, …
Comparing Normal vs Tumor RNAseq data from TCGA
written 11.1 years ago by bn •

<p>Hi, I'm currently looking over RNASeqV2 Level 3 data from TCGA. I was wondering if there were any pitfalls to doing a quick and dirty …