(1) Dpos

Dpos, the first peak-calling algorithm developed in DANPOS, analyzes changes in the location, fuzziness, and occupancy at each nucleosome or protein binding position.

Example 1. Define each nucleosome in MNase-Seq data:

Test data (right click to download and put files in directories as indicated below):

(1) nucleosome_sampleA/

nucleosome_sampleA_rep1.bowtie

nucleosome_sampleA_rep2.bowtie

Command:

python danpos.py dpos nucleosome_sampleA

Example 2. Compare MNase-Seq data at each nucleosome between two samples A and B.

Test data (right click to download and put files in directories as indicated below):

(1) nucleosome_sampleA/

nucleosome_sampleA_rep1.bowtie

nucleosome_sampleA_rep2.bowtie

(2) nucleosome_sampleB.bowtie

Command:

python danpos.py dpos nucleosome_sampleA:nucleosome_sampleB.bed.gz

Example 3. Compare MNase-Seq data at each nucleosome between two samples A and B, with spike-in controls to specify libarary size for each sample.

Test data (right click to download and put files in directories as indicated below):

(1) nucleosome_sampleA/

nucleosome_sampleA_rep1.bowtie

nucleosome_sampleA_rep2.bowtie

(2) nucleosome_sampleB.bowtie

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 dpos nucleosome_sampleA:nucleosome_sampleB.bowtie -c nucleosome_sampleA:10000000,nucleosome_sampleB.bowtie: 20000000

Example 4. Quantile Normalization: Different from DANPOS1, currently, the -n Q parameter for quantile normalization is disabled. If you try to use quantile normalization, first, use dpos function to generate wiq file with -n N parameter, which disable all normalization method and --smooth_width 0 which prevent smooth. Then, you could use "python danpos.py wiq --buffer_size 50 chromosome_size_file yourfileA.wig:yourfileB.wiq" to normalize your file with quantile normalization and call danpos peak caller functions (dpos, dpeak, dregion, dtriple) again. Make sure you always disable -n N and only smooth your data once.