Hi there,
When running bam2cov, I want to use the --runBiasDetection parameter. May I ask if it's necessary to use the biasAnnotationsBedArrayToBeProjected file provided by you? Additionally, I am not sure where this BED file should be added and which parameter it corresponds to. Could you please provide an example?
Another question is, the biasAnnotationsBedArrayToBeProjected file you provided is based on the CHM13 coordinate. If I am using reads aligned to my self-assembled data, should I still use this file?
Thank you very much for your help!
Hi there,
When running bam2cov, I want to use the
--runBiasDetectionparameter. May I ask if it's necessary to use thebiasAnnotationsBedArrayToBeProjectedfile provided by you? Additionally, I am not sure where this BED file should be added and which parameter it corresponds to. Could you please provide an example?Another question is, the
biasAnnotationsBedArrayToBeProjectedfile you provided is based on the CHM13 coordinate. If I am using reads aligned to my self-assembled data, should I still use this file?Thank you very much for your help!