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FelixKrueger · Dec 9, 2024 · 671b2a1 · 671b2a1
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diff --git a/docs/bismark/methylation_extraction.md b/docs/bismark/methylation_extraction.md
@@ -117,6 +117,14 @@ The `coverage2cytosine` module can be instructed that a sample is a NOMe-seq ([*
 
 Both of these measures aim to reduce unwanted biases, i.e. the influence of `G-CG` (intended) and `C-CG` (off-target) on endogenous CpG methylation, and the influence of CpG methylation on (the NOMe-seq specific) `GC` context methylation. **PLEASE NOTE** that NOMe-seq data requires a `.cov.gz` file as input which has been generated in non-CG mode!! (`--CX`), else the `GpC` output file will be empty...
 
+#### (Optional): extract tetra-, penta- or hexamer sequence context
+
+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
@@ -159,6 +159,14 @@ The minimum number of times any methylation state (methylated or unmethylated) h
 
   Writes the output into individual files for each chromosome instead of a single output file. Files are named to include the input filename as well as the chromosome number.
 
+- `--ffs`
+
+  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