Difference between revisions of "Prediction pipeline"
From Crop Genomics Lab.
Line 1: | Line 1: | ||
1. Whole reads were mapped against reference genome | 1. Whole reads were mapped against reference genome | ||
2. Both unmapped reads retrieve using following command | 2. Both unmapped reads retrieve using following command | ||
− | + | ||
− | + | {| class="wikitable" | |
− | + | |- | |
− | + | | samtools view –hb –f 12 –F 256 input.bam > output.bam | |
− | + | ||
+ | |} | ||
3. Make fastq file in bam file using bam2fastq | 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 | 4. Denovo assemble of both unmapped reads using AbySS with k-mer = 51 and q-value = 20 |
Revision as of 07:29, 25 March 2014
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.