I come up to aligning the fastq file based on the reference and as a result, I got the aligned bam file. For the next step, I am going to find an insertion sequence in the specific region of the bam file. Firstly, I checked the site with PCR, and there is an insertion sequence. By the way, when I checked the bam file with bamview, there are no insertion sequences in the region. What is wrong with the steps? I think that the default setting of bwa threw the insertion sequence away.
- bwa index ref.fa;
- bwa aln ref.fa read1.fq > r1.sai;
- bwa aln ref.fa read2.fq > r2.sai;
- bwa sampe ref.fa r1.sai r2.sai read1.fa read2.fq | samtools view -bSho out.bam
- bamview and checked the bam compare to ref.fa
Are you talking about a small (few bp) or large insertion (>50bp)? What is inserted?
The sizes will be larger than 1000bp, it is insertion sequences or so to say transposons. By the way, I found a tool, called "pindel" and dealing with it. Thank you for your interest and I am always opened to your helpful information.