From af935f6fcf6d83c234102fe0317b99976d95206a Mon Sep 17 00:00:00 2001
From: Jose F Oviedo <87445418+josefoviedo@users.noreply.github.com>
Date: Wed, 27 Mar 2024 11:26:27 -0700
Subject: [PATCH 1/2] Update deduplication.md

just some old fashioned deduplication...
---
 docs/bismark/deduplication.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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

From 02efb90dba76f53c2f1ae7ad3e35e4d47a18ee4b Mon Sep 17 00:00:00 2001
From: Jose F Oviedo <87445418+josefoviedo@users.noreply.github.com>
Date: Wed, 27 Mar 2024 11:43:40 -0700
Subject: [PATCH 2/2] Update methylation_extraction.md

function name edit in docs
---
 docs/bismark/methylation_extraction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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: