Dpuiu snp: Difference between revisions
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cat frag.mated.soap2 | sort -k8 -nk9 >! frag.mated.soap2.sorted | cat frag.mated.soap2 | sort -k8 -nk9 >! frag.mated.soap2.sorted | ||
mv frag.mated.soap2.sorted frag.mated.soap2 | mv frag.mated.soap2.sorted frag.mated.soap2 | ||
soapsnp -i frag.mated.soap2 -d genome.fasta -o genome.cns | soapsnp -i frag.mated.soap2 -d genome.fasta -o genome.cns | ||
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bowtie-build genome.fasta genome.fasta | bowtie-build genome.fasta genome.fasta | ||
bowtie genome.fasta -1 frag_1.fastq -2 frag_2.fastq -p 8 -I 120 -X 240 --sam > frag.mated.sam | bowtie genome.fasta -1 frag_1.fastq -2 frag_2.fastq -p 8 -I 120 -X 240 --sam > frag.mated.sam | ||
samtools view -bS frag.mated.sam > frag.mated.bam | samtools view -bS frag.mated.sam > frag.mated.bam | ||
Revision as of 15:13, 1 June 2011
Links
Soap
- Example:
2bwt-builder genome.fasta soap2 –a frag_1.fastq -b frag_2.fastq -D genome.fasta.index -o frag.mated.soap2 -2 frag.single.soap2 -m 120 -x 240 cat frag.mated.soap2 | sort -k8 -nk9 >! frag.mated.soap2.sorted mv frag.mated.soap2.sorted frag.mated.soap2 soapsnp -i frag.mated.soap2 -d genome.fasta -o genome.cns
Bowtie/Samtools
bowtie-build genome.fasta genome.fasta bowtie genome.fasta -1 frag_1.fastq -2 frag_2.fastq -p 8 -I 120 -X 240 --sam > frag.mated.sam samtools view -bS frag.mated.sam > frag.mated.bam samtools sort frag.mated.bam frag.mated.bam.sorted mv frag.mated.bam.sorted frag.mated.bam
samtools mpileup -ugf genome.fasta frag.mated.bam | bcftools view -vcg - > genome.snps