v0.20.0
bismark_methylation_extractor
-
The methylation extractor now creates output directories if they don't exist already.
-
The options
--ample_mem
and--buffer_size <string>
are now mutually exclusive. -
Changed the directory being passed on when
--cytosine_report
is specified from parent directory' to 'output directory'.
bismark2report
- Major rewrite of
bismark2report
: HTML file are now rendered using Plotly.js[plotly.js v1.39.4]
which is completely open source and free to use. Highcharts and JQuery were dropped, as was raised here: #177.
The filesbioinfo.logo
,bismark.logo
,plot.ly
andplotly_template.tpl
are read in dynamically from a new folder plotly.bismark_sitrep
and all its contents no longer ship with Bismark. The Bismark HTML reports should be completely self-contained, here is an example paired-end Bismark report.
bismark2summary
- Major rewrite of
bismark2summary
: HTML file are now rendered using Plotly.js[plotly.js v1.39.4]
which is completely open source and free to use. Highcharts and JQuery were dropped, as was raised here: #177. The filesbioinfo.logo
,bismark.logo
,plot.ly
andplotly_template.tpl
are read in dynamically from a new folder plotly.bismark_sitrep
and all its contents no longer ship with Bismark. The Bismark HTML Summary reports should be completely self-contained, here is an example of a percent alignment plot for a single cell experiment:
.
And finally, here are some examples for a WGBS summary report, an RRBS report (no deduplication), and the full scBS-seq report and scBS-seq data file.