break parameter

[jwli-code]

When running CRAQ, I didn't pay attention to using the --break=T parameter, and now I have completed all the results. How can I generate the Break sequence?

[JiaoLaboratory]

The out_final.CSE.out file records all potential structural error loci. If the -break parameter was not used in advance, you can execute the following command based on the result file:

$ perl CRAQ/src/break_at_Misjunction.pl Genome.fa runAQI_out/strER_out/out_final.CSE.out > out_correct.fa