Strandness

[Mark Rassner]

Hello all, I'm having a problem with visualization of -SS same vs. -SS opposite strand reads (in stranded RNA-Seq libraries).

First, I noticed that those two flaggs gave almost the same result. When I use two different bed files (one form "+", the other from "-" genes), they DO differ, dramatically (however, same and opposite looks almost the same for both of them).

I'm hence wondering, how to solve this issue? Given that my input is >18k genes, I'd expect "+" and "-" genes to look similar, but not "-SS same" and "-SS opposite".

Has this been adressed elsewhere?

Thanks to everyone and kind regards

Mark

[Dahun]

I'm not a developer but I can suggest some tips for your problem.

I think you should check your library. For first-stranded library, R2 is RNA direction. So, you should keep in mind that strand is opposite. If you check the strandness of library, then you can split the BAM files following their strandness. I suggest you make plots for using split BAM files. How about using other visualization tools such as HOMER(annotatePeaks) or Deeptools(plotProfile)? I think it is easier to use than ngsplot.

2025년 10월 28일 화요일 오후 9시 27분 3초 UTC+9에 ugol...@gmail.com님이 작성: