At least according to the documentation, it seems for WGS you can use the `batch --method wgs` option. There is more information here: [https://cnvkit.readthedocs.io/en/stable/nonhybrid.html][1] which also includes some extra options and notes. This will calculate the needed targets on the fly if there is not one provided - though if you only want i.e....

It is the consensus for all reads that overlap a given base, it's not a genome consensus unless your reads cover the entire genome.

Hello everyone, I need to call the CNV from my hunam WGS data. I searched for many tutorial, but I did'nt get any proper procedure. I am trying to call the CNV using CNVkit. Can any one tell me the procedure and in that cnvkit pipeline there is a file called bait.bed file used as (-t TARGETS) option. where will get that file. Do I need to generate on...

Hi All, I am facing following error in single cell analysis using seurat package, error is while plotting PCA and violin plot: > Error in Ops.data.frame(guide_loc, panel_loc) : ‘==’ only defined or equally-sized data frames I am using ggplot2 version 3.5.1 and seurat version 5.0.1 Thank you, Sumeet

I don't think dropout is playing an important role with Malat1 since it is usually highly expressed. On the other hand, if dropout is still a concern for you, Malat1-negative cells tend to cluster, so you can remove those clusters.

Resolved by increasing heapsize of -Xmx50G