Embedded Files
Example 1. Define each enriched region, peak, and nucleosome for histone modification H3K4me3 in a single sample, with input effect subtracted:
Test data (right click to download and put files in directories as indicated below):
(1) H3K4me3_sampleA/
(2) input_sampleA/
Command:
python danpos.py dtriple H3K4me3_sampleA -b input_sampleA
Example 2. Compare H3K4me3 ChIP-Seq data between two samples A and B, each sample has its own input effect to be subtracted.
Test data (right click to download and put files in directories as indicated below):
(1) H3K4me3_sampleA/
(2) input_sampleA/
(4) input_sampleB/
Command:
python danpos.py dtriple H3K4me3_sampleA:H3K4me3_sampleB.bed.gz -b H3K4me3_sampleA:input_sampleA,H3K4me3_sampleB.bed.gz:input_sampleB
Example 3. Compare H3K4me3 ChIP-Seq data between two samples A and B, with spike-in controls to specify libarary size for each sample, each sample has its own input effect to be subtracted.
Test data (right click to download and put files in directories as indicated below):
(1) H3K4me3_sampleA/
(2) input_sampleA/
(4) input_sampleB/
Spike-ins information:
Suppose that we have spike-ins to indicate that there would be 10 and 20 million reads for sample A and B, respectively.
Command:
python danpos.py dtriple H3K4me3_sampleA:H3K4me3_sampleB.bed.gz -b H3K4me3_sampleA:input_sampleA,H3K4me3_sampleB.bed.gz:input_sampleB -c H3K4me3_sampleA:10000000,input_sampleA:10000000,H3K4me3_sampleB.bed.gz:20000000, input_sampleB:20000000
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