A function for primary mapping of short reads with bowtie and the conversion of the SAM output into BAM format In the actual implementation it is possible to run bowtie using pair-end fastq files produced using Illumina platform. The available reference sets are built for human, hs, mouse, mm and rat, rn. Analysis is performed chromosome by chromosome to limit RAM consumption. In the present implementation bowtie runs with the following parameters: -a –best -k 1 -q -v 3 -S. Therefore only the first best alignment is shown, imput files are in fastq format, alignment up to three mismatches are considered and the output is in SAM format. At the end of the mapping SAM files are converted in BAM files using picard tools.
Raffaele A Calogero
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