rcavalcante
commented
8 years ago - An update with lots of minor tweaks.
- 705a1e9 Change PePr default threshold to 1e-05, minimum read length of 25bp for trim_galore, reduce multicore default for bismark_methylation_extractor, 0.05 FDR for methylSig significance with methylation difference of 10.
- 560e4e7 Remove coannotation plots from annotatr results. Takes too long for real data.
- eebb3f1 Write bowtie2 stderr to file to get alignment frequencies
- b83af40 Add mint version to top of makefile
- 0a7646f CpG report _for_methylSig.txt and _for_annotatr.txt are now INTERMEDIATE
- f32eb42 Save R sessions for methylSig and annotatr as .RData in /RData
- 60a90d1 Missed some PePr nomenclature changes
- A number of commits to make temporary file cleanup rule, clean_tmp
- Create _for_methylSig.txt file in the bisulfite_compare module instead of the bisulfite_align module.
- 3de4819 Change annotatr rule target from the first .png output to the .RData of the session.
- 2d0383a Add global OPT_MIN_COV variable that applies to the bismark_methylation_extractor and preparation for sample_classification.
- 84b43a5 Add region width plots for simple classification and PePr
- 9ea83b1 Add MACS2 model.pdf creation