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Reads mapping

In ncPRO-seq, http://bowtie-bio.sourceforge.net/index.shtml Bowtie ($ <$v2) [9] is used to align reads to the reference genome. Different bowtie options can be specified to map different formats of reads: BOWTIE_GENOME_OPTONS_FQ for fastq reads, BOWTIE_GENOME_OPTIONS_FA for fasta reads and BOWTIE_GENOME_OPTIONS_CS for csfasta reads. Bowtie outputs alignments in SAM format, which are then converted to BAM format by using http://samtools.sourceforge.net/ SAMtools [10].

Both BAM files from read alignment and from input BAM file pre-processing step will be used to generate figure files summarizing mapping information: mapping statistics and mapped read size distribution. In the mapping statistics figure, the proportions of reads with unique and multiple mapping sites in the genome, and unmapped reads are plotted.


Nicolas Servant 2012-05-31