Visualize pileup data

Question

[bsmith030465]

Hi,

I have a pileup file that contains the read information for overlaps on GFP data. Is there an online tool where I can upload the pileup file and the reference .fa file to visualize the data?

Or is there a program that I can download to visualize this data?

thanks!

[Friederike]

Not sure what GFP data is and what type of visualization you're after, but have you tried IGV for a start?

Answer 1

[Sehi L'Yi]

Potentially helpful resources:

• IGV: https://igv.org/
• JBrowse: https://jbrowse.org/jb2/
• HiGlass PileUp Track: https://github.com/higlass/higlass-pileup
• Gosling.js: https://gosling.js.org/?example=BAM_PILEUP

Answer 2

[atorreso]

The list provided by Sehi L'Yi is probably the way to go, but I will also add the R package Gviz which it's also useful for figures.