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Visualizing BS-converted Read Mapping

The tview subcommand allows the user to visualize mappings generated by BISCUIT. biscuit tview is similar to samtools tview, but includes additional coloring for reads that have undergone bisulfite conversion. Because of this additional coloring, a reference FASTA file is required for biscuit tview so that bisulfite conversion can be identified.

$ biscuit tview my_input.bam /path/to/my_reference.fa

tview screenshot

In the reference, CpGs are marked in red, while C’s and G’s in other contexts are marked in blue. For reads, retained C’s/G’s are marked in red, while converted C’s/G’s are marked in blue. Mismatches not related to bisulfite conversion are marked in yellow.

For more help on the available options, run biscuit tview in the terminal or visit the tview help page.