Using parameter -q indicates reads are fastq format with fasta as default. I believe VALET treats the reads as fastq by default, and likely requires reads in fastq format. Using the -q parameter causes and error with breakpoint finder. Proposed solution is to remove the -q parameter from the options and require fastq file as input.
Using parameter
-qindicates reads are fastq format with fasta as default. I believe VALET treats the reads as fastq by default, and likely requires reads in fastq format. Using the-qparameter causes and error with breakpoint finder. Proposed solution is to remove the-qparameter from the options and require fastq file as input.