Question

Problem in loading multiple BAM files in IGV

1

Entering edit mode

2.0 years ago

askif4 ▴ 20

I recently re-installed IGV and I have trouble loading multiple BAM files.

It looks like this.

enter image description here

What option do I have to choose to solve this problem?

WGS IGV BAM • 1.8k views

ADD COMMENT • link updated 2.0 years ago by Ram 44k • written 2.0 years ago by askif4 ▴ 20

1

Entering edit mode

buy a much wider screen or load less BAM. ¯\_(ツ)_/¯

ADD REPLY • link 2.0 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

Exactly (assuming the screen is already rotated, otherwise you need a higher screen xD).

As a work-around I could think of: merge bams and give each of them a distinct read group, and group/split the window by read-groups.

ADD REPLY • link 2.0 years ago by yhoogstrate ▴ 150

1

Entering edit mode

cross posted : https://bioinformatics.stackexchange.com/questions/20141

ADD REPLY • link 2.0 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

askif4 Don't post on multiple forums, it's bad etiquette.

ADD REPLY • link 2.0 years ago by Ram 44k

score 0 · Answer 1 · 2022-12-08

If its just the problem that you want to see the alignment while zoomed out. IGV zoom into alignment Go to View > Preferences. Then in Alignments tab, change the Visibility range threshold field.

If the bam files are too big it can slow down IGV and you may have to also increase the memory that the program is allowed to use.

There is also next to "human hg19" a drop down menu to go to the contig/chromosome you want to view. However, is "human hg19" also the reference to which you mapped? If not you need to separately upload your reference sequence and select it to view your alignments.