I have a
.bam file generated by the aligner
minimap2 (included in the EPI2ME online service from Oxford Nanopore; I am using the MinION for sequencing).
I sorted it and indexed it using
samtools sort align.bam
samtools index sort.bam
I then dragged and dropped
sort.bam in IGV. It seemed to load it fine, but I cannot see any of my reads... They are supposed to mostly align to one gene, I can find the reference gene, but no sign of any reads there.
Additional troubleshooting I have tried so far:
- I think
minimap2is using hg38 while the default reference in IGV is hg19. So I also tried loading the hg38 in IGV as reference (
Load genomes from server), but still cannot see anything in the expected region.
- I have converted my
samtools view test.bam -o test.sam) so I could scroll through it. I think all looks good, and most of the reads do mention my gene of interest. Does the
.samfile include any chr:position I could use to figure out where to look in IGV?