Difference between revisions of "Prediction pipeline"

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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"
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:|-
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{| class="wikitable"
:| samtools view –hb –f 12 –F 256 input.bam > output.bam
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|-
:
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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
 
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.