diff --git a/docs/bismark/deduplication.md b/docs/bismark/deduplication.md index 34e5c80..657f500 100644 --- a/docs/bismark/deduplication.md +++ b/docs/bismark/deduplication.md @@ -26,7 +26,7 @@ In addition to chromosome, start (and end position for paired-end libraries) pos MISEQ:14:000000000-A55D0:1:1101:18024:2858_1:N:0:CTCCT ``` -This option option is equivalent to using [UmiBam](https://github.com/FelixKrueger/Umi-Grinder) in the following mode: +This option is equivalent to using [UmiBam](https://github.com/FelixKrueger/Umi-Grinder) in the following mode: `UmiBam --umi input.bam`, however UmiBam has additional functionality such as a double UMI feature or the option to allow mismatches in the UMI(s). ### Deduplication of multiple files of the same library diff --git a/docs/bismark/methylation_extraction.md b/docs/bismark/methylation_extraction.md index 622bd72..4db84a0 100644 --- a/docs/bismark/methylation_extraction.md +++ b/docs/bismark/methylation_extraction.md @@ -89,7 +89,7 @@ The main difference to the `bedGraph` or `coverage` output is that **every** cyt #### GpC methylation assessment: Context-specific methylation summary report -Every time `coverage2cyyosine` is run, the counts for each cytosine context are recorded and printed to a special file called `*.cytosine_context_summary.txt` for each input coverage file. +Every time `coverage2cytosine` is run, the counts for each cytosine context are recorded and printed to a special file called `*.cytosine_context_summary.txt` for each input coverage file. The report ([introduced here](https://github.com/FelixKrueger/Bismark/issues/321)) looks at 2 bp downstream, as well as 1 bp upstream of the cytosine taking part in the methylation call. This is useful for looking at methylation in specific contexts (e.g. `CpA` only), and also when using `GpC` methylases that introduce methylation in `GpC` context. The report looks like this: