Hi!

I have nanopore sequencing results in fastq format. I need to know the coverage of specific genes. To do this, I aligned the sequence using minimap2 and converted the result to bam format. I want to use the Samtools view to extract the gene by coordinate. Then I plan to use the Samtools depth.

The command to run after alignment looks like this:

1. samtools view -h myFile.sam -b -o fastq_pass/myFile.bam
2. samtools sort myFile.bam -o myFile_sort.bam
3. samtools index myFile_sort.bam
4. samtools view myFile_sort.bam chr22:41865129-41924993 > myGene.bam
5. samtools depth myGene.bam > myGene.bam_bepth

I want to extract the sequence from region chr22:41865129-41924993 . But when opening a file with a gene coverage depth, the start and end coordinates are shifted:

chr22   41863407    1
chr22   41863408    1
chr22   41863409    1
...
...
...
chr22   41932508    1
chr22   41932509    1
chr22   41932510    1
chr22   41932511    1

Could someone please tell me what I'm doing wrong.