(r2) RunningAligners < BETA

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Assume for all instances below that a single FASTA reference =ref.fasta= and a single FASTQ read file =reads.fastq= are in the same directory as the program executable

Running [[http://bowtie-bio.sourceforge.net/tutorial.shtml][bowtie]]:
   * Build the index
      * =bowtie-build ref.fasta reference=
   * Single-end alignments
      * =bowtie -S reference reads.fastq output.sam= (=-S= required for SAM output)

Running [[http://bio-bwa.sourceforge.net/bwa.shtml][bwa]]
   * Build the index
      * =bwa index ref.fasta=
   * Single-end alignment
      * =bwa aln ref.fasta reads.fastq > output.sai=
   * Convert to SAM
      * =bwa samse ref.fasta output.sai reads.fastq > output.sam=

Running [[http://bioinformatics.bc.edu/marthlab/Mosaik][Mosaik]]
   * Build the index
      * =MosaikBuild -fr ref.fasta -oa ref.dat=
   * Convert the reads
      * =MosaikBuild -q reads.fastq -out reads.dat -st illumina= (=illumina= is the machine the reads were produced by)
   * Single-end alignments
      * =MosaikAligner -in reads.dat -out output.dat -ia ref.dat -hs 14 -act 17 -mm 2 unique=
   * Convert to SAM
      * =MosaikText -in output.dat -sam output.sam=

Note that the above was adapted from the =Build= and =Align= scripts from in the =data= directory of the Mosaik download.

If all went well, you should obtain an =output.sam= file, using any of the above programs...

You can then display this using [[http://samtools.sourceforge.net/][SAMTools]]:
   * Index the reference
      * =samtools faidx ref.fasta=
   * Convert SAM to BAM
      * =samtools import ref.fasta output.sam output.bam=
   * Sort the BAM (orders the reads by positions in the reference)
      * =samtools sort output.bam sorted= (will create =sorted.bam=)
   * Index the sorted BAM (unsorted BAM files cannot be indexed)
      * =samtools index sorted.bam=
   * Display
      * =samtools tview sorted.bam ref.fasta=

On a side note, you can convert a BAM file to a SAM file like so:
   * =samtools view sorted.bam > sorted.sam=


As typing these can be a real pain, I actually automate the process using batch files...
Topic revision: r2 - 2010-05-05 - jayzhang