Difference between revisions of "Sequence Alignment"

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

@@ Line 14: / Line 14: @@
 '''Build FM index'''
-    $ bowtie2-build ''CDS.fasta'' ''CDS.fasta''
+    $ 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''