Merge pull request #665 from josefoviedo/master

Update deduplication.md
FelixKrueger · Mar 27, 2024 · 37e2cad · 37e2cad
2 parents acf965c + 02efb90
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diff --git 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
@@ -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: