IGV genome browser problems
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8.7 years ago
Marvin ▴ 220

Hi,

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): reads.fastq

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 >blablabla

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.

igv • 4.3k views
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Think you will need to actually learn how to use the programme before accusing it for not being useful.

There are a lot of possible reason. For the last part of the question where you don't have the update, it is likely that you haven't got the new fasta indexed. Without that, IGV most likely used the old index and therefore give you the old name information.

As for the read not appearing. It might be best for us to actually see the bam file. Is it possible for us to have the header of the fasta e.g. >blablabla and the bam header (you can obtain it by typing samtools view -H aln_sorted.bam)

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Sorry, I was really frustrated earlier.

You were right Sam, I didn't have the new index although the command to build a new index is in my python script. But 'bwa index' doesn't build a new index if the file already exists as I have found out now. So that's the reason for the wrong chromosome name.

And the reason for the unseen reads is even simpler: I didn't zoom in close enough + there are very few mappings after all (aDNA reads). I didn't expect to see much but I didn't expect to see nothing. But it's even stated in the browser itself: 'Zoom in to see alignments'. That would almost be funny if it wasn't so embarrassing. Thanks for the help!

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IGV has a substantial usability issue here - the visual marker that states that you need to zoom in is written in light gray, small font and it is very easy to miss. Especially for newcomers there is a visual overload there with lots of other visual cues everywhere. Nothing to be ashamed of.

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If the data load correctly, you may need to navigate to a region of interest by, for example, zooming or searching, before you see any features.

I think you need to spend some time with the user guide and/or a video tutorial.

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