Difference between revisions of "Prediction pipeline"
From Crop Genomics Lab.
(Created page with "# Whole reads were mapped against reference genome # Both unmapped reads retrieve using following command {| class="wikitable" |- | samtools view –hb –f 12 –F 256 input....") |
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− | + | 1. Whole reads were mapped against reference genome | |
− | + | 2. Both unmapped reads retrieve using following command | |
− | {| class="wikitable" | + | :{| class="wikitable" |
− | |- | + | :|- |
− | | samtools view –hb –f 12 –F 256 input.bam > output.bam | + | :| 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. |
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
- |}