downsampling problem

[­심원 / 학생 / 치의과학과]

Hello,

I'm using igv_linux_2.11.4

I loaded my RNA-seq bam file which I aligned to the reference genome.

The coverage track and alignment track seem fine, but I found that some regions with low coverage number displays more aligned read.

I guess it's because of downsampling, but the problem is that I cannot change that option.

When I go into View->Preferences->ThirdGen, 'downsample reads' option is already disabled.

Apart from that, any settings I change in the View->Preference doesn't affect the displayed data.

What's the problem?

Thanks.

[James Robinson]

I don't understand your description of the problem, and am unsure if downsampling is involved or not, but it you want to change the downsampling option do it in the "alignments" tab.   The ThirdGen tab is for 3rd gen data (i.e. long reads like pacbio and ont).

[­심원 / 학생 / 치의과학과]

Thank you for your prompt reply.

I changed the downsampling option in the "alignments" tab, and the problem was solved.

Thank you.

2021년 12월 17일 금요일 오전 7시 43분 15초 UTC+9에 James Robinson님이 작성: