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align_handson [2012/12/10 15:51]
evidal 		align_handson [2017/05/24 14:23] (current)
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 +====== Alignment: Practical session ======
  
 +\\
 +
 +<code bash>
 +#!/bin/bash
 +
 +#move and create directory
 +cd ~/mda12
 +mkdir -p mapping
 +
 +# index reference
 +time bwa index resources/ref/human_g1k_v37.chr20.fasta
 +time samtools faidx resources/ref/human_g1k_v37.chr20.fasta
 +
 +# align pair 1
 +time bwa aln -t 1 -l 40 -k 2 resources/ref/human_g1k_v37.chr20.fasta\
 + resources/data/test_1.fq >\
 + mapping/test_1.sai
 +
 +# align pair 2
 +time bwa aln -t 1 -l 40 -k 2 resources/ref/human_g1k_v37.chr20.fasta\
 + resources/data/test_2.fq >\
 + mapping/test_2.sai
 +
 +# merge Paired-End in SAM
 +time bwa sampe -n 1\
 + resources/ref/human_g1k_v37.chr20.fasta mapping/test_1.sai mapping/test_2.sai\
 + resources/data/test_1.fq  resources/data/test_2.fq >\
 + mapping/test.sam
 +
 +# SAM to BAM conversion
 +time samtools view -bS mapping/test.sam -o mapping/test.bam
 +
 +# basic stats all reads
 +time samtools flagstat mapping/test.bam | tee mapping/flagstat_all.txt
 +
 +# sort and index BAM
 +time samtools sort mapping/test.bam mapping/test_sorted
 +time samtools index mapping/test_sorted.bam
 +
 +# filter alignment
 +time samtools view -S -h -F 4 -q 10 mapping/test.sam | grep -v "XA:Z:" > mapping/test_mapped.sam
 +
 +# SAM to BAM conversion
 +time samtools view -bS mapping/test_mapped.sam -o mapping/test_mapped.bam
 +
 +# basic stats mapped reads
 +time samtools flagstat mapping/test_mapped.bam | tee mapping/flagstat_mapped.txt
 +
 +# sort and index BAM
 +time samtools sort mapping/test_mapped.bam mapping/test_mapped_sorted
 +time samtools index mapping/test_mapped_sorted.bam
 +
 +# bamQC
 +/home/biouser.23-10-2012/mda12/qualimap/qualimap
 +
 +# IGV
 +igv
 +</code>