From 25c9a093f68c7e63f200d5deb31da3c6d339b857 Mon Sep 17 00:00:00 2001 From: Felix Krueger Date: Mon, 9 Dec 2024 10:06:25 +0000 Subject: [PATCH] formatting --- docs/bismark/methylation_extraction.md | 4 +++- docs/options/methylation_extraction.md | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/docs/bismark/methylation_extraction.md b/docs/bismark/methylation_extraction.md index bcb0708..abb963e 100644 --- a/docs/bismark/methylation_extraction.md +++ b/docs/bismark/methylation_extraction.md @@ -121,10 +121,12 @@ Both of these measures aim to reduce unwanted biases, i.e. the influence of `G-C The `coverage2cytosine` module can be instructed to also extract a **f**our-, **f**ive- and **s**ix-nucleotide context (`--ffs`) for cytosines in question. Hexamers follow the rule `xxCxxx`. Too short sequences (e.g. at the edges of the chromosome) are left blank; sequences containing Ns are ignored. + ``` Example: U00096.3 90 + 0 0 CG CGT CGTG CGTGA GCCGTG U00096.3 91 - 1 0 CG CGG CGGC CGGCA CACGGC - + ``` + ### M-bias plot Starting with Bismark v0.8.0, the Bismark methylation extractor also produces a methylation bias plot which shows the methylation proportion across each possible position in the read (described in further detail in: [Hansen et al., Genome Biology, 2012, 13:R83](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-10-r83)). The data for the M-bias plot is also written into a coverage text file (ending in `.cov` or `.cov.gz`) and is in the following format: diff --git a/docs/options/methylation_extraction.md b/docs/options/methylation_extraction.md index b89a5cf..9802114 100644 --- a/docs/options/methylation_extraction.md +++ b/docs/options/methylation_extraction.md @@ -163,10 +163,12 @@ The minimum number of times any methylation state (methylated or unmethylated) h In addition to the standard output this option also extracts a **f**our-, **f**ive- and **s**ix-nucleotide context for the cytosines in question. Hexamers follow the rule `xxCxxx`. Too short sequences (e.g. at the edges of the chromosome) are left blank; sequences containing Ns are ignored. This option needs to be run via `coverage2cytosine` itself. + ``` Example: U00096.3 90 + 0 0 CG CGT CGTG CGTGA GCCGTG U00096.3 91 - 1 0 CG CGG CGGC CGGCA CACGGC - + ``` + #### OUTPUT ##### Extractor output