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How to find where reads mapped along reference

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.

next-gen alignment sequencing
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updated by lieven.sterck lieven.sterck • written by joshua.eunsong.craig • joshua.eunsong.craig

1 answer

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

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written by lieven.sterck lieven.sterck

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