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AstraZeneca-NGS / disambiguate

Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
MIT License
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disambiguate and bowtie #14

Open kmavrommatis opened 5 years ago

kmavrommatis commented 5 years ago

Hi, do you have any suggestions on how to use disambiguate with Bowtie and Bowtie2?

Thanks K

mjafin commented 5 years ago

Hi @kmavrommatis, Thanks for the note. Tophat ultimately uses Bowtie/Bowtie2 as the underlying aligner. The tophat option uses tags XO, NM and NH. I cannot remember if Bowtie produces all the same flags. If it does, you could just select Tophat as the option. (However I suspect not all the three flags get produced by Bowtie.)

I don't currently have plans to add support for bowtie/bowtie2. I would strongly suggest using bwa-mem instead as it's far superior as an aligner and will give you much better disambiguation results.

Hope this helps some.