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Differences between results example_chr22 and test_chr22

We compared our results on the small test example to the expected results using meld, and found that the results are identical except for least significants digits in some cases.

In ABC Output/Neighborhoods

$ l test_chr22/ABC_output/Neighborhoods/
EnhancerList.bed
EnhancerList.txt
Enhancers.DHS.wgEncodeUwDnaseK562AlnRep1.chr22.bam.CountReads.bedgraph
Enhancers.DHS.wgEncodeUwDnaseK562AlnRep2.chr22.bam.CountReads.bedgraph
Enhancers.H3K27ac.ENCFF384ZZM.chr22.bam.CountReads.bedgraph
GeneList.bed
GeneList.TSS1kb.bed
GeneList.txt
Genes.DHS.wgEncodeUwDnaseK562AlnRep1.chr22.bam.CountReads.bedgraph
Genes.DHS.wgEncodeUwDnaseK562AlnRep2.chr22.bam.CountReads.bedgraph
Genes.H3K27ac.ENCFF384ZZM.chr22.bam.CountReads.bedgraph
Genes.TSS1kb.DHS.wgEncodeUwDnaseK562AlnRep1.chr22.bam.CountReads.bedgraph
Genes.TSS1kb.DHS.wgEncodeUwDnaseK562AlnRep2.chr22.bam.CountReads.bedgraph
Genes.TSS1kb.H3K27ac.ENCFF384ZZM.chr22.bam.CountReads.bedgraph

Changes list:

  • `ABC Output/NeighborhoodsEnhancerList.bed`: 4 minor differences (one-digit change/line) among 3330 lines
  • EnhancerList.txt: a lot of minor changes (lists reordered) among 3331 lines
  • Enhancers.DHS.wgEncodeUwDnaseK562AlnRep1.chr22.bam.CountReads.bedgraph: 4 minor changes (one-digit change/line) among 3277 lines
  • Enhancers.DHS.wgEncodeUwDnaseK562AlnRep2.chr22.bam.CountReads.bedgraph: 4 minor changes (one-digit change/line) among 3330 lines
  • Enhancers.H3K27ac.ENCFF384ZZM.chr22.bam.CountReads.bedgraph: 4 minor changes (one-digit change/line) among 3330 lines
  • GeneList.TSS1kb.bed: 2*2 minor changes (lines with identical loci swapped)

The remaining 8 files are identical to their other version. Note that almost all digit-changes were simply a value incremented or decremented by 1 (and the others were in/decremented by 2).

In ABC Output/Peaks

$ l test_chr22/ABC_output/Peaks/
params.txt
wgEncodeUwDnaseK562AlnRep1.chr22.macs2_model.r
wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak
wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.sorted
wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.sorted.candidateRegions.bed
wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.sorted.wgEncodeUwDnaseK562AlnRep1.chr22.bam.Counts.bed
wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.xls
wgEncodeUwDnaseK562AlnRep1.chr22.macs2_summits.bed

Changes list:

  • params.txt is different from its original version but the differences arincremented be expected path differences
  • wgEncodeUwDnaseK562AlnRep1.chr22.macs2_model.r: A lot of difference, but all of them are due to the increased number of significative digits in our test version

This fact is very likely to explain the observed one-digit changes in ABC Output/Neighborhoods.

  • wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak: a lot of changes (generally 1, 2 or 3 significative-digits changes ; sometimes more)
  • wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.sorted: idem
  • wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.sorted.candidateRegions.bed: 4 minor differences (one-digit change/line) among 3330 lines

Indeed, this explains all one-digit change in ABC Output/Neighborhoods.

  • wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.sorted.wgEncodeUwDnaseK562AlnRep1.chr22.bam.Counts.bed: files are identical
  • wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.xls: a lot of changes, same as wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak. Another (expected) change is path in the header, and one comment deleted.
  • wgEncodeUwDnaseK562AlnRep1.chr22.macs2_summits.bed: a lot of changes, same as wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.

In ABC_output/Predictions

$ l example_chr22/ABC_output/Predictions/
EnhancerPredictionsAllPutativeNonExpressedGenes.txt.gz  EnhancerPredictionsFull.txt
EnhancerPredictionsAllPutative.txt                      EnhancerPredictions.txt
EnhancerPredictionsAllPutative.txt.gz                   GenePredictionStats.txt
EnhancerPredictions.bedpe                               parameters.predict.txt

cd example_chr22/ABC_output/Predictions/
meld <name> ../../../test_chr22/ABC_output/Predictions/<name>
  • EnhancerPredictionsAllPutativeNonExpressedGenes.txt.gz: a lot of minor changes (last or last few significant digits)
  • EnhancerPredictionsAllPutative.txt.gz: a lot of minor changes (last or last few significant digits)
  • EnhancerPredictionsAllPutative.txt: the file only exists in example_chr22, not in our test
  • etc