visualizing the Shallow whole genome sequencing on the UCSC

Question

[Sara]

I have a Shallow whole genome sequencing data set and aligned that using bwa. I am trying to visualize the data on the UCSC. first I made wig file but they are so big to be uploaded then I made bedgraph file and managed to upload them on the UCSC but the coverage is so low. here you find a screenshot of the UCSC. do you know what the problem is or how I can make a better visualization of reads on the genome.

[AK]

Hi Sara, I think you need to change the picture markdown to:

[ucsc_example][1]

  [1]: https://i.ibb.co/Cv8dk2Q/ucsc.png

[ATpoint]

Yep, please also see How to add images to a Biostars post, made the changes for you this time.

[ATpoint]

How did you generate that track? I would go with deeptools bamCoverage to get a bigwig track.

[Sara]

@ ATpoint: thanks. do you know how I can find copy numbers (CNVs)?

[ATpoint]

There are many tools for this available. Please use google and the search functions for recommendations and papers.

Answer 1

[bernatgel]

Hi Sara,

If you have shallow WGS you'll probably want to plot a whole genome view or at least a chromosome-wide view. You can create these plots in R with karyoploteR using the kpBAMDensity function:

library(karyoploteR)
bam.file <- "path/to/your/bam"

kp <- plotKaryotype()
kpPlotBAMDensity(kp, bam.file)

You can plot more than one sample in the same image using r0 and r1 and you can customize the appearance of the data in many ways. You can find more information in karyoploteR's vignette or in the tutorial page.