Bismark Summary Reports
Please Note: This script has now been incorporate into Bismark, see the bismark documentation for reference. Also note that MultiQC (http://multiqc.info) performs much the same task as well as supporting other tools.
Bismark is a tool used for aligning Bisfulfite-Sequencing libraries, giving information about DNA methylation.
For every sample that is analysed, Bismark produces statistics such as alignment rates and methylation calls. A report is generated to show this data, fantastic for interrogating single samples. It is of less use when a large number of samples are processed in parallel, however (as is increasingly the norm).
This script takes a list of bismark-processed BAM files as an input, looks for the corresponding bismark reports and produces a HTML summary report. The report is interactive, allowing the data to be plotted with absolute counts or percentages. Methylation calls can be shown in CpG, CHG and CHH context.
In addition to the HTML report, a text file is generated with tab delimited numbers for post-processing.
See the full example report here: bismark_summary_report.html
You can also see the tab-delimted text file here: bismark_summary_report.txt
perl bismark_summary_report.pl *.bam
This script is run on the command line. There are currently no customisation options.
The script is written in Perl and run on the command line.
For more information, please get in touch with Phil Ewels.