--- a/README.md
+++ b/README.md
@@ -1,42 +1,36 @@
-# MethodsTBS
-
-Targeted Bisulfite Sequencing for Biomarker Discovery
-
-## Processing Scripts
-
-- Scripts for processing targeted bisuflite sequencing data written for use with SGE cluster environment
-  - Adapter Trimming
-  - Indexing
-  - Read alignment
-  - Methylation Calling
-
-## Analysis Notebooks
-
-- Jupyter notebook describing
-  - Quality Control Pipeline
-  - Fitting Epigenetic Clock Using Targeted Bisulfite Sequencing Data
-
-## Targeted Bisulfite Sequencing QC
-
-The code to produce the following graphs is contained in the QC jupyter notebook. The goal of the QC analysis is to
-assess alignment performance by looking at general alignment statistics, the number of reads mapping to regions
-targeted by the probes, and the observed duplication rate.
-
-### Alignment QC
-
-We can start assessing alignment quality by looking at the output logs generated by the alignment tool
-[BSBolt](https://bsbolt.readthedocs.io/en/latest/). The alignment log give information on the total number of read pairs
-observed, the bisulfite strand where reads mapped, and the number of unmapped reads / bisulfite ambiguous alignments. The
-mappability is calculated as $mappability = 2 * total read pairs - unmapped reads$.
-
-![png](imgs/bsb_alignment_log_stats.png)
-
-Using *bedtools multicov* we will investigate the average number of reads that map to the targeted regions. The coverage
-shown is plotted for all mapped reads and mapped reads with duplicates removed.
-
-![png](imgs/bedtools_multicov.png)
-
-Using *samtools flagstat* we can investigate the alignment file by looking at the sam flags set for each read. Sam flags are bitwise combination of different alignment attributes. Coverage information taken from the *bedtools multicov* has been combined
-with the *flagstat* output to provide additional details.
-
-![png](imgs/sam_flagstat.png)
+# MethodsTBS
+
+Targeted Bisulfite Sequencing for Biomarker Discovery
+
+## Processing Scripts
+
+- Scripts for processing targeted bisuflite sequencing data written for use with SGE cluster environment
+  - Adapter Trimming
+  - Indexing
+  - Read alignment
+  - Methylation Calling
+
+## Analysis Notebooks
+
+- Jupyter notebook describing
+  - Quality Control Pipeline
+  - Fitting Epigenetic Clock Using Targeted Bisulfite Sequencing Data
+
+## Targeted Bisulfite Sequencing QC
+
+The code to produce the following graphs is contained in the QC jupyter notebook. The goal of the QC analysis is to
+assess alignment performance by looking at general alignment statistics, the number of reads mapping to regions
+targeted by the probes, and the observed duplication rate.
+
+### Alignment QC
+
+We can start assessing alignment quality by looking at the output logs generated by the alignment tool
+[BSBolt](https://bsbolt.readthedocs.io/en/latest/). The alignment log give information on the total number of read pairs
+observed, the bisulfite strand where reads mapped, and the number of unmapped reads / bisulfite ambiguous alignments. The
+mappability is calculated as $mappability = 2 * total read pairs - unmapped reads$.
+
+Using *bedtools multicov* we will investigate the average number of reads that map to the targeted regions. The coverage
+shown is plotted for all mapped reads and mapped reads with duplicates removed.
+
+Using *samtools flagstat* we can investigate the alignment file by looking at the sam flags set for each read. Sam flags are bitwise combination of different alignment attributes. Coverage information taken from the *bedtools multicov* has been combined
+with the *flagstat* output to provide additional details.