visualization.txt

bowtie2-build -f  Trypanosoma_cruzi_Dm28c.fasta Trypanosoma_cruzi_Dm28c

bowtie2 --score-min 'C,0,-1' -x Trypanosoma_cruzi_Dm28c -f TryTrypDB_Aug2017_alltRNAs.tfam.fas -S aligned.sam

Inorder to get the perfect matches With bowtie2, you can either just use "grep AS:i:0" or just use the "--score-min 'C,0,-1'" option, which should do effectively the same thing.


samtools view -b -S -o aligned.bam aligned.sam

samtools sort aligned.bam aligned.sorted

samtools index aligned.sorted.bam

samtools tview aligned.sorted.bam Trypanosoma_cruzi_Dm28c.fasta Trypanosoma_cruzi_Dm28c.fasta

Tablet seems a better visualization tool.