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droog_22 02-09-2012 08:53 AM

Simulating paired-end reads and bowtie alignments

I am simulating paired-end read data by extracting 36-mers from the dm3 genome and generating pairs of reads which are 550 bp apart. I then use bowtie to map the paired-end data like this:

bowtie -p 12 --ff -f -X 2000 -v 0 -m 1 --quiet dm3.index -1 reads_1.fasta -2 reads_2.fasta
The strange think is that I would expect the fragment lengths of the mapped reads to be exactly 550bp, however I do see a distribution of fragments lengths with a peak around 550. How can this be? Should bowtie not find the exact location in the genome from where is was generated or does it use a kind of penalty or heuristic which would explain this behavior?

My goal is just to find mappable regions in the genome given paired-end sequencing data with a certain fragment length.

Reads, Daniel

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