Changes

Sequence Analysis Practice 2011/03/09 (view source)

33 bytes removed , 17:09, 9 March 2011

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2. Align using BWA

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${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \

+

${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon.sample.read1.fastq.gz > ${OUT}/NA12878.exon.sample.read1.fastq.gz.sai

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${IN}/NA12878.exon.sample.read1.fastq.gz \

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> ${OUT}/NA12878.exon.sample.read1.fastq.gz.sai

−

${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \

+

${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon.sample.read2.fastq.gz > ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai

−

${IN}/NA12878.exon.sample.read2.fastq.gz \

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> ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai

−

${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \

+

${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon.sample.unpaired.fastq.gz ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai

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${IN}/NA12878.exon.sample.unpaired.fastq.gz \

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> ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai

${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa \

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