Is it possible for juicer using Bowtie2 to map reads instead of bwa ?

aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

http://aidenlab.org

MIT License

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Is it possible for juicer using Bowtie2 to map reads instead of bwa ? #307

Open AssumeAssume opened 1 year ago

AssumeAssume commented 1 year ago

Are you sure this is an issue? Github Issues is reserved for situations that require changes to the codebase. Questions, discussions, etc. should be posted to the forum: aidenlab.org/forum.html Hello,

I want to map fastq with bowtie2 in the juicer pipeline, is there any possibility for us to change bwa with bowtie2 ?

Thanks