I have a bam file aligned to a reference sequence. I am interested in finding the number of reads for read length 18 to 34, where the last base is mis-matched. I got this bam file from bowtie alignment allowing 3 mismatches (-v 0) option, so I am expecting some of the reads to have terminal bases mis-matched. How can we count the number of sequences of a specific length with terminal mismatch in bam file?
I have created a bowtie aligned .sam file with this command:
bowtie -S -p 18 /media/owner/ref.fa test1.fastq test1.sam
which I then converted to .bam file like this:
samtools view -bS -o test1.bam test1.sam
From this test1.bam, I was able to get the total number of plus and minus strand of reads aligned to the reference loci using bedtools coverage maping (for positives reads and negative reads) like this:
bedtools coverage -a my_region.bed -b test1.bam -bed -d -s | gzip > test1_region_pos.tsv.gz
Since I used default bowtie option which allows for three mismatches, I want to know how many reads are aligned with terminal mismatches (i.e,last three, last two and last one base mismatched at 3' region of the aligned reads at their loci position).