Implement system in config to allow for alternative aligners with a SAM/BAM standardized output. This will likely require the user to know a little about snakemake as they would need to write the 'run' statement in the correct format, example could be provided with bwa.
Additionally, an analysis script would need to be put together that will output the same / similar file types to that of couple.R (uniq.csv, multihit.rds, chimeras.rds). This script would need to be written following the practices of the Bushman lab.
Implement system in config to allow for alternative aligners with a SAM/BAM standardized output. This will likely require the user to know a little about snakemake as they would need to write the 'run' statement in the correct format, example could be provided with bwa.
Additionally, an analysis script would need to be put together that will output the same / similar file types to that of couple.R (uniq.csv, multihit.rds, chimeras.rds). This script would need to be written following the practices of the Bushman lab.