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....") |
Revision as of 04:52, 24 March 2014
- Whole reads were mapped against reference genome
- Both unmapped reads retrieve using following command
| samtools view –hb –f 12 –F 256 input.bam > output.bam |
- Make fastq file in bam file using bam2fastq
- Denovo assemble of both unmapped reads using AbySS with k-mer = 51 and q-value = 20
- Denovo assemble of whole sequencing reads using AbySS with k-mer = 51 and q-vale = 20
- 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
