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Troubleshooting

The only parameters that should be necessary to change are in the top section with

DIRECTORY=/mnt/research/germs/Schuyler/Projects/X
RAWDAT_DIRECTORY=$DIRECTORY/original
MAPPING_FILE=$RAWDAT_DIRECTORY/map.txt
CORES=20

OVERLAP=10
MINLENGTH=210 
MAXLENGTH=280
Q=10
CLUSTER=0.99

Feel free to explore other parameters within the code. As long as you have the raw data backed-up, there is no commands in this pipeline that should be able to make unfixable mistakes.

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