@@ -169,7 +169,7 @@ roi <- range(tx) + 1e6

 @ 

 Next we get the genetic sequence and use it to create a GmapGenome

-object. (Please note that the TP53_demo GmapGenome object is used by

+object. (Please note that the TP53\_demo GmapGenome object is used by

 many examples and tests in the gmapR and VariationTools packages. If

 the object has been created before, its subsequent creation will be

 instantaneous.)

@@ -273,7 +273,7 @@ genome <- TP53Genome()

 The \software{LungCancerLines} R package contains a BAM file of reads

 aligned to the TP53 region of the human genome. We'll use this file to

-demonstrate the use of \software{bam_tally} through the

+demonstrate the use of \software{bam\_tally} through the

 \software{gmapR} package. The resulting data structure will contain

 the needed information such as number of alternative alleles, quality

 scores, and nucleotide cycle for each allele.