diff --git a/README.md b/README.md
index 36441d5..2112234 100644
--- a/README.md
+++ b/README.md
@@ -20,16 +20,26 @@ in its documentation hosted on [ReadTheDocs](http://japsa.readthedocs.org/en/lat
 ## Usage
 
 Before running capsim, the probe sequences need to be aligned to the reference sequence (or the genome sequence to simulate sequencing). We recommend using bowtie2 for the alignment.
+   
+    #Skip this step if the index has been generated
+    bowtie2-build ref.fasta ref
+    
+    #Align the probes into the reference
+    bowtie2 --local --very-sensitive-local --mp 8 --rdg 10,8 --rfg 10,8 -k 10000 -f -x ref -U probes.fa -S probes.sam
 
-After alignment, sort the and index the bam file
+Note: for some reason, bowtie2 only accepts the query fasta file (probes.fa) containing one sequence per line.
+
+After alignment, sort the and index the bam file with samtools
+
+     samtools view -bSU probes.sam | samtools sort -o probes.bam -
 
 Capsim takes the bam file as the input:
 
-    jsa.sim.capsim --reference ref.fasta --probe probe.sam --ID someid --fmedian 5000  --pacbio output --pblen 3000 --num 20000000
+    jsa.sim.capsim --reference ref.fasta --probe probes.bam --ID someid --fmedian 5000  --pacbio output --pblen 3000 --num 20000000
 
 or 
 
-    jsa.sim.capsim --reference ref.fasta --probe probe.sam --ID someid --fmedian 500  --miseq output --illen 300 --num 20000000
+    jsa.sim.capsim --reference ref.fasta --probe probes.bam --ID someid --fmedian 500  --miseq output --illen 300 --num 20000000