Difference between revisions of "Prediction pipeline"

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(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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# Whole reads were mapped against reference genome
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1. Whole reads were mapped against reference genome
# Both unmapped reads retrieve using following command
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2. Both unmapped reads retrieve using following command
{| class="wikitable"
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:{| class="wikitable"
|-
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:|-
| samtools view –hb –f 12 –F 256 input.bam > output.bam
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:| samtools view –hb –f 12 –F 256 input.bam > output.bam
 
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:
|}
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:|}
# Make fastq file in bam file using bam2fastq
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3. Make fastq file in bam file using bam2fastq
# Denovo assemble of both unmapped reads using AbySS with k-mer = 51 and q-value = 20
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4. 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
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5. 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
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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
#
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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
|}
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.