f5c
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When doing f5c call-methylation, the quality of dorado basecaller's reads was significantly lower than that of guppy basecaller's reads
This is the full log of the f5c call-methylation:
This is dorado basecaller's order:
dorado basecaller /share/home/yzwl_hanxs/app/dorado-0.5.3-linux-x64/model/[email protected] ./pod5/ | amtools view -bhS -@ 10 > test.bam
Convert bam to fastq:
samtools fastq -0 test.fastq test.bam
Use minimap2 to align:
minimap2 -a -x map-ont /share/home/yzwl_hanxs/refdata-gex-GRCh38-2020-A/fasta/genome.fa test.fastq | samtools sort -o test.sorted.bam -T test.tmp
This is the log for minimap2:
Why does this happen
Thank you,
ShengquanWang