RNAseq: reads in different positions in IGV vs IGB

Question

[Roman Hillje]

Hi guys,

I'm currently working on some scRNAseq data and looked for reads in my BAM file that mapped over a known mutation we found in that sample. So first I used bamtools intersect to check if there are any reads that overlap the mutation and found that there should be a few in JAK2. Then I wanted to inspect them visually in a genome browser and used IGV because that's what I've used so far. Interestingly, no reads overlap the position of interest. When I load the same BAM file into IGB however I see what I expected.

I made sure to select hg19 in both cases.

Does anybody have an idea what's going on here?

I attached screenshots so you get an idea of what I'm talking about.

IGB https://ibb.co/k6TY3G

IGV https://ibb.co/nujjAw

Thanks, Roman

[ATpoint]

Please check the preferences of the IGV to make sure that no cutoff for e.g. minimal mapping quality is set. See here for details.

[Mason Meyer]

Hello,

My name is Mason Meyer, IGB Support Specialist. I viewed your attached screenshots and am not sure why this issue is occurring, but I am happy to assist you in achieving your desired visualization using IGB. If you have any questions, please let me know. You can contact me directly, if you'd like, by e-mailing our team through the link on the IGB support page.

Also, if you are interested in a demo of how to get started using IGB, I would be happy to help out!

Thanks,

Mason Meyer, IGB Support Specialist