Input fastq file

[andreanperry]

Should the input fastq file to BLAZE be a basecalled file (for example, I am using Dorado to do the basecalling, which generates a .bam file I can convert to fastq) or should alignment also be done so that the input to BLAZE is a basecalled and aligned fastq file?

[youyupei]

Hi @andreanperry , BLAZE doesn't work on BAM files. As the alignment information would be removed anyway when you convert bam to fastq, there wouldn't be much difference whether the reads were aligned or not.