Igv alignment showing question mark symbol (?) instead of the sequences(ATCG) in tracks

[Shreya Dey]

I have a reference genome (fasta file) and certain bam files which are mapped against the reference genome. While I load the bam files in igv, it does shows the position but the sequences are not visible, instead it shows a question mark. I have checked the cigar string it gives me correct details but visualisation in igv isn't working somehow. Has anyone encountered this issue earlier.

Image for reference attached. 

[James Robinson]

That looks like an alignment, not the reference sequence.  This probably means the read sequence is not included in your bam record.   Its optional, read sequence is not required in "bam" files.

[Shreya Dey]

Hey there,

Thanks for the heads up. I want to include the read sequences in the bam files for further processing. I'm using minimap2. Is there any way I can include them. I'm new to this, any help will be much appreciated :)

[James Robinson]

First we should verify that's the problem.   If you right-click over the alignments a long menu will popup.  Near the bottom is an option to "Export Alignments".    This will export the alignments currently in view to a file.  Select this and save the file, zip it, and attach it here or email it to igvteam (at) broadinstitute.org and I will have a look.

[Robert King]

I have this same issue, what was the solution?

[James Robinson]

Robert, I would ask you the same thing.  Could you export a sample of your alignments as instructed and send them to us?   I suspect the read sequence is not stored in your bam files.

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[robin...@gmail.com]

There is another thread on this topic,   I suspect the read sequence for the alignments in question is not stored in your BAM file.   It looks like minimap2 does not store read sequence for secondary alignments.   In any event, if the read sequence is not stored IGV cannot know it, and displays ?.    See https://github.com/lh3/minimap2/issues/4

If you don't think this is the case please post the alignment details here, which you can get my clicking on the alignment.   

[Uljana Hesse]

It happens when the same read mapped at two locations