Hello,
I performed nanopolish index, followed by alignment using minimap2 and call methylation using nanopolish and received output, which is in some binary format, not in TSV with columns as shown on the Nanopolish docs.
I have attached the head of the output I received.
Can you please tell me where I could have gone wrong? Because this data works well with Bonito and Dorado to call bases and modifications.
Thank you.
I have used the following commands:
INDEXING: nanopolish index -d HG00733_ONT_CeNT.fastq
ALIGNMENT : /minimap2 -a -x map-ont hg38.fa HG00733_ONT_CeNT.fastq | /home2/sfglab/sgadakh/anaconda3/bin/samtools sort -T tmp -o HG00733_ONT_CeNT.sorted.bam /home2/sfglab/sgadakh/anaconda3/bin/samtools index HG00733_ONT_CeNT.sorted.bam
Hello, I performed nanopolish index, followed by alignment using minimap2 and call methylation using nanopolish and received output, which is in some binary format, not in TSV with columns as shown on the Nanopolish docs. I have attached the head of the output I received. Can you please tell me where I could have gone wrong? Because this data works well with Bonito and Dorado to call bases and modifications. Thank you.
I have used the following commands:
INDEXING: nanopolish index -d HG00733_ONT_CeNT.fastq
ALIGNMENT : /minimap2 -a -x map-ont hg38.fa HG00733_ONT_CeNT.fastq | /home2/sfglab/sgadakh/anaconda3/bin/samtools sort -T tmp -o HG00733_ONT_CeNT.sorted.bam /home2/sfglab/sgadakh/anaconda3/bin/samtools index HG00733_ONT_CeNT.sorted.bam
METHYLATION CALLING : nanopolish call-methylation -r HG00733_ONT_CeNT.fastq -b HG00733_ONT_CeNT.sorted.bam --genome hg38.fa --methylation cpg -o methy_733_ontcent.tsv
The head of output of "methy_733_ontcent.tsv" has content shown in the attached image.