Permute? or no?

This post covers brief findings from exploring permutation tests when looking for differentially methylated genes from whole genome bisulfite sequencing. The idea behind it: if we randomly shuffle the data between control and treatment samples and see roughly the same number of genes coming out as differentially methylated then we can't say the genes we originally … Continue reading Permute? or no? →

Integration of Rstudio and GitHub

There is a free course you can take online that shows you how to: Set up a GitHubMake citable DOI's to each repository Integrate Rstudio and push your code directly to GitHub through git I found this course extremely useful. It comes in three segments, addressing the above, each with an easy to follow video. … Continue reading Integration of Rstudio and GitHub →

Notifications for new blog posts

If you follow the blog you'll get notifications to let you know about new posts - by default this takes the form of an email every time someone posts something. You can control the frequency of the notifications by going here while logged in and changing the settings for this blog. You can switch between … Continue reading Notifications for new blog posts →

BS-seq problems – the solution

In the previous post I described a problem with BS-seq data. After much messing about I found the solution in the analysis tool methylKit. Rather than using the final output of the Bismark aligner tool (the 'coverage' or 'cytosineReport' files) you can use methylKit to process the BAM file Bismark makes in order to generate a file … Continue reading BS-seq problems – the solution →

Bisulfite sequencing – bad tiles on the flowcell

Recently I've had a great deal of difficulty with some BS-seq data, which had some bad reads where the quality dropped off randomly in the middle of the sequence - this is unusual as quality issues are typically at the ends of reads. You can see this illustrated below. The poor quality reads seem to … Continue reading Bisulfite sequencing – bad tiles on the flowcell →