add mapping section and fix links

sipbs-compbiol · Feb 13, 2025 · 0f4caed · 0f4caed
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diff --git a/_quarto.yml b/_quarto.yml
@@ -49,6 +49,8 @@ book:
       chapters: 
         - fastqc.qmd
         - trimmomatic.qmd
+
+    - part: mapping.qmd
 
     - references.qmd
 

diff --git a/mapping.qmd b/mapping.qmd
@@ -0,0 +1,3 @@
+# Read Mapping {@sec-mapping .unnumbered}
+
+There are several approaches to comparison of genome sequences. One method is to align (or _map_) the sequenced reads from one genome to a different, reference genome. Reads will only _map to_ (align with) sequence-similar regions, so it is possible to inspect the alignments and see which parts of the two genomes are similar or dissimilar.
diff --git a/trimmomatic.qmd b/trimmomatic.qmd
@@ -66,4 +66,4 @@ You can inspect the contents of these files by clicking on the filename in the `
 
 ## Next steps
 
-Now that we have clean, high-quality sequencing reads, we can move on to mapping the reads to a reference genome, in @sec-map-reference.
+Now that we have clean, high-quality sequencing reads, we can move on to mapping the reads to a reference genome, in @sec-mapping.
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		@@ -0,0 +1,3 @@
		# Read Mapping {@sec-mapping .unnumbered}

		There are several approaches to comparison of genome sequences. One method is to align (or _map_) the sequenced reads from one genome to a different, reference genome. Reads will only _map to_ (align with) sequence-similar regions, so it is possible to inspect the alignments and see which parts of the two genomes are similar or dissimilar.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -66,4 +66,4 @@ You can inspect the contents of these files by clicking on the filename in the `

		## Next steps

		Now that we have clean, high-quality sequencing reads, we can move on to mapping the reads to a reference genome, in @sec-map-reference.
		Now that we have clean, high-quality sequencing reads, we can move on to mapping the reads to a reference genome, in @sec-mapping.