How to find where reads mapped along reference

Question

[joshua.eunsong.craig]

Hello,

I sequenced some strains of Ensifer medicae and have mapped them to the reference WSM419 using bwa. Afterwhich I sorted, reordered, etc. using picard. What I want to find out is where along the reference my reads mapped to, as I want to compare and visualize the location and percent of reads mapped between strains (Some strains mapped 85%, some 25%, I want to visualize this if possible).

While IGV is useful, I ideally want to be able to visualize whole chromosomes and plot each strain's coverage around it in circularized plots.

Thanks.

Answer 1

[lieven.sterck]

Without knowing the specific details on how you would like to have it plotted, it sounds like a job circos should be able to handle