Difference between revisions of "Sequence Alignment"
From Crop Genomics Lab.
Sangrea Shim (Talk | contribs) |
Sangrea Shim (Talk | contribs) |
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'''Build FM index''' | '''Build FM index''' | ||
− | $ bowtie2-build '' | + | $ bowtie2-build ''ref.fasta'' ''ref.fasta'' |
+ | |||
+ | |||
+ | '''Reads Alignment''' | ||
+ | |||
+ | $ bowtie2 -x ''ref.fasta(FM index)'' -U ''unpaired.fastq.gz'' -S ''output.sam'' | ||
+ | |||
+ | |||
+ | '''Converting Sequence Alignment/Mapping file(SAM) to Binary Sequence Alignment/Mapping file(BAM)''' | ||
+ | |||
+ | $ samtools view -bS ''input.sam'' > ''output.bam'' | ||
+ | |||
+ | |||
+ | '''Build fasta index''' | ||
+ | |||
+ | $ samtools faidx ''ref.fasta'' | ||
+ | |||
+ | |||
+ | '''Sorting BAM file''' | ||
+ | |||
+ | $ samtools sort ''input.bam'' ''output.bam'' | ||
+ | |||
+ | |||
+ | '''Pileup and variant calling ''' | ||
+ | |||
+ | $ samtools mpileup -DSugf ''ref.fasta'' ''input.bam'' |bcftools view -vcg - > ''output.vcf'' |
Latest revision as of 06:19, 17 December 2014
Sequence Alignment
Materials: Mungbean CDS sequence file(FASTA), Transcriptome sequence of mungbean Softwares: BOWTIE2, samtools
Pick CDS sequences which is located on Vradi01 chromosome
using your own python code or $ tr '\n' '\t' < Vradi_ver6.fa.cds.primary.fasta |sed 's/\t>/\n>/g' |grep 'Vradi01g' |tr '\t' '\n'
Build FM index
$ bowtie2-build ref.fasta ref.fasta
Reads Alignment
$ bowtie2 -x ref.fasta(FM index) -U unpaired.fastq.gz -S output.sam
Converting Sequence Alignment/Mapping file(SAM) to Binary Sequence Alignment/Mapping file(BAM)
$ samtools view -bS input.sam > output.bam
Build fasta index
$ samtools faidx ref.fasta
Sorting BAM file
$ samtools sort input.bam output.bam
Pileup and variant calling
$ samtools mpileup -DSugf ref.fasta input.bam |bcftools view -vcg - > output.vcf