I have never used IGV before.
I have a reference:
reference.fa (bacterial, no chromosomes, just one '>' line)
I have reads (actually only a small subset for testing):
I map the reads against the reference with bwa. I check the bam file and see that the first read matches at position 1 in the genome (because I have actually copied the sequence) -> CIGAR string = 70M
All as expected.
Then I load the genome via Load Genome
Then I load the
aln_sorted.bam via Load File
Then I see: Nothing. No mappings, just nothing. Why?
I delete the genome via Manage Genome List (And also the
aln_sorted.bam track via Remove)
I change the header line of the reference to
Then I load the reference again via Load Genome
In the 'select chromosome' dropdown it still shows me the old chromosome name. But that name does not even exist anymore! I have reloaded the reference with a new chromosome name.