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!
