Processing report

bismark report (classic alias: bismark2report) uses a Bismark alignment report, and optionally further reports of the Bismark suite such as deduplication, methylation extractor (splitting) or M-bias reports to generate a graphical HTML report page.

If several Bismark reports are found in the same folder, a separate report will be generated for each of these, whereby the output filename is derived from the Bismark alignment report file.

bismark report attempts to find optional reports automatically based on the file basename.

Example reports

You can see an example single-end report and paired-end report.

Usage

bismark report [options]

Options

• -o/--output <filename> (optional)

Name of the output file. If not specified explicitly, the output filename will be derived from the Bismark alignment report file. Specifying an output filename only works if the HTML report is to be generated for a single Bismark alignment report (and potentially additional reports).

• --dir <directory> (optional)

Output directory. Default: current directory.

• --alignment_report FILE (optional)

If not specified, bismark report attempts to find Bismark report file(s) in the current directory and produces a separate HTML report for each mapping report file. Based on the basename of the Bismark mapping report, bismark report will also attempt to find the other Bismark reports (see below) for inclusion into the HTML report.

Note

Although the option is optional (as bismark can try to detect the filename automatically), including a Bismark alignment report file is mandatory.

• --dedup_report FILE (optional)

If not specified, bismark report attempts to find a deduplication report file with the same basename as the Bismark mapping report (generated by bismark dedup) in the current working directory.

Including a deduplication report is optional, and using the FILE none will skip this step entirely.

• --splitting_report FILE (optional)

If not specified, bismark report attempts to find a splitting report file with the same basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current working directory.

Including a splitting report is optional, and using the FILE none will skip this step entirely.

• --mbias_report FILE (optional)

If not specified, bismark report attempts to find a single M-bias report file with the same basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current working directory.

Including an M-Bias report is optional, and using the FILE none will skip this step entirely.

• --nucleotide_report FILE (optional)

If not specified, bismark report attempts to find a single nucleotide coverage report file with the same basename as the Bismark mapping report (generated by Bismark with the option --nucleotide_coverage, or bismark bam2nuc directly) in the current working directory.

Including a nucleotide coverage statistics report is optional, and using the FILE none will skip this report entirely.