Question: Why Bowtie2 and Lastz give so different results?
gravatar for gbdias
4.9 years ago by
gbdias90 wrote:

Hey guys,

I'm mapping 50 bp reads from several ChIP-seq datasets to a short reference (170bp). I want to measure the relative enrichment of this specific consensus in the different IP conditions. It's repetitive DNA so I guess it's ok to use a consensus.

To do so, I used Bowtie2 (with the --end-to-end and --local modes) and Lastz (with the 12of19 seed and no filtering).

The number of reads mapping to my reference in all datasets (about 30 ngs files) was always bigger when I used Lastz. I can understand why bt2 end-to-end VS local give different results. But shouldn't Lastz and bt2 --local give comparable results?

Should I apply filtering to the Lastz mapping?

lastz chip-seq alignment bowtie2 • 1.2k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by gbdias90
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