Revision as of 01:44, 31 May 2010

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Get Reference Genome

Merge all the reference sequences into one fasta file hg18.fasta (?) Index the reference genome:

  bwa index -a bwtsw hg18.fasta

-l Take the first INT subsequence as seed

-q Parameter for read trimming.

 bwa aln -l 32 -q 15 -foutput1.aln hg18.fasta file1.fastq.gz
 bwa aln -l 32 -q 15 -foutput2.aln hg18.fasta file2.fastq.gz

Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.

 bwa sampe hg18.fasta output1.aln output2.aln file1.fastq.gz file2.fastq.gz >  output.sam

 samtools view output.sam >  output.bam

 samtools sort output.bam sorted_prefix

@@ Line 1: / Line 1: @@
 {{RRedon}}
+=Get Reference Genome=
+Download the hg18/build36 from UCSC: [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/ http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes]
+=get SamTools=
+[http://samtools.sourceforge.net/ http://samtools.sourceforge.net/]
+=With BWA=
+* [http://bio-bwa.sourceforge.net http://bio-bwa.sourceforge.net]
+Merge all the reference sequences into one fasta file hg18.fasta (?)
+Index the reference genome:
+   bwa index -a bwtsw hg18.fasta
+==Pre mapping==
+* extract every 500th read from fastq file
+* Align one fastq files
+'''-l'''  Take the first INT subsequence as seed
+'''-q'''  Parameter for read trimming.
+  bwa aln -l 32 -q 15 -foutput1.aln hg18.fasta file1.fastq.gz
+  bwa aln -l 32 -q 15 -foutput2.aln hg18.fasta file2.fastq.gz
+* Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.
+  bwa sampe hg18.fasta output1.aln output2.aln file1.fastq.gz file2.fastq.gz >  output.sam
+* export to bam
+  samtools view output.sam >  output.bam
+* sort bam
+  samtools sort output.bam sorted_prefix
+=With MAQ=
+* [http://maq.sourceforge.net/ http://maq.sourceforge.net/]