I've used minimap2 to map my HiFi reads (with MM and ML tags) with my reference genome.
$ minimap2 -ax map-pb -Y scaffolds_final.fa HiFi.fastq > aln_CpG.sam
I've converted the sam alignment file to a sorted, indexed bam file using samtools:
When running pb-CpG-tools using the indexed bam file, I get a BW file and an empty BED file. I am unsure if I am "losing" the MM and ML tags somewhere in the process... I have used the "soft clipping" option for minimap.
Hi !
I've used minimap2 to map my HiFi reads (with MM and ML tags) with my reference genome. $ minimap2 -ax map-pb -Y scaffolds_final.fa HiFi.fastq > aln_CpG.sam
I've converted the sam alignment file to a sorted, indexed bam file using samtools:
$ samtools view -Sb -o aln_CpG.bam aln_CpG.sam $ samtools sort -O bam -o sorted_aln_CpG.bam aln_CpG.bam $samtools index sorted_aln_CpG.bam
When running pb-CpG-tools using the indexed bam file, I get a BW file and an empty BED file. I am unsure if I am "losing" the MM and ML tags somewhere in the process... I have used the "soft clipping" option for minimap.
Any ideas about what might be the issue?
Thanks!