getDifferentialPeaksReplicates.pl Output on Up/Dn regulated in target
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Entering edit mode
8 weeks ago
yee • 0

Hello BioStars community, I've finished running HOMER's script on running differential peaks enrichment (with replicates) and I noticed a lot of my histone data had a bunch of up-regulated genes reported and often zero down-regulated genes to report? I'm pretty new to bioinformatics, and I'm not sure if this is an issue with data quality or is this normal for histone analysis?

Hopefully, this isn't too dumb of a question.

Here is my code and output. I was provided only one input/igG (control) but multiple replicates:

getDifferentialPeaksReplicates.pl \
  -genome hg38 \
  -style histone \
  -DESeq2  -t \
  /mnt/e/S-group/sorted/FINAL_bam_output/tag_directories/rep1 \
  /mnt/e/S-group/sorted/FINAL_bam_output/tag_directories/rep2 \
  /mnt/e/S-group/sorted/FINAL_bam_output/tag_directories/rep3 \
  -i /mnt/e/S-group/sorted/FINAL_bam_output/tag_directories/Input \
  > H3K4me4_input_diff_peaks.txt
  Step3: Calling R for differential enrichment statistics (-DESeq2)

        Autodetecting input file format...
        Autodetected annotatePeaks.pl file

        Performing variance stabalization (rlog)...

        Using DESeq2 to calculate differential expression/enrichment...
        Output Stats input vs. target:
                Total Genes: 27340
                Total Up-regulated in target vs. input: 19209 (70.260%) [log2fold>1, FDR<0.05]
                Total Dn-regulated in target vs. input: 0 (0.000%) [log2fold<-1, FDR<0.05]
HOMER DESeq2 • 142 views
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