1. Whole reads were mapped against reference genome 2. Both unmapped reads retrieve using following command
|samtools view –hb –f 12 –F 256 input.bam > output.bam|
3. Make fastq file in bam file using bam2fastq 4. Denovo assemble of both unmapped reads using AbySS with k-mer = 51 and q-value = 20 5. Denovo assemble of whole sequencing reads using AbySS with k-mer = 51 and q-vale = 20 6. BLASTN between contigs derived from whole sequencing reads and those derived from both unmapped reads which are longer than 2k with e-value threshold, 1e-100 7.