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Add BowTie2 support #257
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Recommended maping settings for aDNA: https://academic.oup.com/mbe/article/35/5/1120/4844088 Additional for UDG treatment and looking for methylation: https://www.frontiersin.org/articles/10.3389/fevo.2020.00105/full#B4 |
Ok, changed my mind on this one. We should include it in 2.2 because it would be important for eager1 parity and also given the Poullet and Orlando paper, would make it more relevent. I will try to contact the authors and get their recommendations. |
Docker building here in the repository could also be added then, if we anyways play around with the dev container adding bowtie2 now too |
Bowtie2 dependency is added too. Remaining would be to allow for alternative mapper instead of bwa ;-) |
https://www.frontiersin.org/articles/10.3389/fevo.2020.00105/full So we should enable at least that mode if possible :-) |
Is your feature request related to a problem? Please describe.
This was previously in EAGER1, but also has benefit of "better for investigating absent gene regions since it can split the reads when mapping." (requested by Ash V. in CPH)
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