From Crop Genomics Lab.
1. Whole reads were mapped against reference genome
2. Both unmapped reads retrieve using following command
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- | samtools view –hb –f 12 –F 256 input.bam > output.bam
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- |}
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.
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