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shimlab / BLAZE

SingleCell Nanopore sequencing data analysis
GNU General Public License v3.0
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Input fastq file #22

Open andreanperry opened 2 months ago

andreanperry commented 2 months ago

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 commented 2 months ago

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.