bowtie2 only writes reads to a single target

ibest / ARC

Assembly by Reduced Complexity (ARC)

Apache License 2.0

41 stars 5 forks source link

bowtie2 only writes reads to a single target #30

Closed samhunter closed 10 years ago

samhunter commented 11 years ago

Bowtie2 is being run in default mapping mode which means it only report one hit. Add the ability for reporting multiple hits (-k switch).

This has been implemented and is in need of testing.

samhunter commented 10 years ago

This appears to be working fine. If you set: bowtie_2k=1 in the ARC_config.txt, it will run in default bowtie2 single (hopefully best) target mode. The default (if nothing is entered in ARC_config.txt) is to report up to 5 hits.