Sequence Alignment

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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
  $ 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