Hey,
I'm so confused with my m6A analysis results, very much appreciated it if someone could help me solve it!
I sent my RNA samples to a company that did the MeRIP experiment for me. I had input and ip fastq files, I did trim using trimgalore, and alignment with STAR, the unique mapping reads are all 40-50%
and I found those multi-mapping reads are from ribosome-RNA. Then I used those bam files to do the peak calling with Exomepeak, and then got the differentiated m6A files .csv. Then I input those bam files obtained from STAR into IGV, trying to find some examples to present. But there are many hypermethylated genes shown in the m6A files .csv that were hypomethylated shown in IGV.
Does anybody have the same issue? and does anybody know how to fix it? Thanks so much!
Best,
Lu
