RNAseq: reads in different positions in IGV vs IGB
Entering edit mode
4.0 years ago
Roman Hillje ▴ 40

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

RNA-Seq igv igb • 1.5k views
Entering edit mode

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.

Entering edit mode


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!


Mason Meyer, IGB Support Specialist


Login before adding your answer.

Traffic: 2695 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6