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align_handson [2012/12/10 15:51] evidal |
align_handson [2017/05/24 14:25] (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> |