A few examples of using dLEM CLI on input data¶

• Get input data
• Simplest run and look at small region
• Middle example, multiple regions many chromosomes
• Everythign example, all chromosomes, plots, cool, and track output

Grab test data¶

Download the test data, using Drosophila Melanogaster dataset from (https://elifesciences.org/articles/94070)[Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion]. Using the lambda control as input to dLEM.

In [ ]:

%%bash

mkdir -p ../data
cd ../data
wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE263nnn/GSE263229/suppl/GSE263229%5FGlambdaLmerged.mcool

%%bash mkdir -p ../data cd ../data wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE263nnn/GSE263229/suppl/GSE263229%5FGlambdaLmerged.mcool

Fix data¶

In [ ]:

hictk fix-mcool ./data/GSE263229_GlambdaLmerged.mcool GSE263229_GlambdaLmerged_fix.mcool

hictk fix-mcool ./data/GSE263229_GlambdaLmerged.mcool GSE263229_GlambdaLmerged_fix.mcool

Run dLEM -- Small¶

Run dLEM for generating tracks on a small area (Hox cluster) in Drosophila

In [ ]:

%%bash

dlem --output-tracks \
    --norm -l 1600 \
    --device cpu \
    -r chr3R:6552201-7088853 \
    GSE263229_GlambdaLmerged_fix.mcool \
    ../tests/drosophila_test_small/

%%bash dlem --output-tracks \ --norm -l 1600 \ --device cpu \ -r chr3R:6552201-7088853 \ GSE263229_GlambdaLmerged_fix.mcool \ ../tests/drosophila_test_small/

In [1]:

!head ../tests/drosophila_test_small/chr3R_6552201_7088853_pred_left.bed

!head ../tests/drosophila_test_small/chr3R_6552201_7088853_pred_left.bed

chr3R	6552000	6553600	0.9496542811393738
chr3R	6553600	6555200	0.9546419978141785
chr3R	6555200	6556800	0.9068929553031921
chr3R	6556800	6558400	0.9515242576599121
chr3R	6558400	6560000	0.9534903168678284
chr3R	6560000	6561600	0.9707276821136475
chr3R	6561600	6563200	0.9189634323120117
chr3R	6563200	6564800	0.9149964451789856
chr3R	6564800	6566400	0.9269620776176453
chr3R	6566400	6568000	1.0

In [2]:

!head ../tests/drosophila_test_small/chr3R_6552201_7088853_pred_right.bed

!head ../tests/drosophila_test_small/chr3R_6552201_7088853_pred_right.bed

chr3R	6552000	6553600	0.9556282162666321
chr3R	6553600	6555200	0.9982491135597229
chr3R	6555200	6556800	1.0
chr3R	6556800	6558400	0.9977637529373169
chr3R	6558400	6560000	0.9901233315467834
chr3R	6560000	6561600	0.9918801784515381
chr3R	6561600	6563200	1.0
chr3R	6563200	6564800	0.9430415034294128
chr3R	6564800	6566400	0.8898563385009766
chr3R	6566400	6568000	0.9278128147125244

Run dLEM -- Medium¶

In [ ]:

%%bash

dlem --output-tracks \
    --plot \
    --norm \
    -l 1600 \
    --device cpu \
    -b ../tests/in_regions.bed \
    GSE263229_GlambdaLmerged_fix.mcool \
    ../tests/drosophila_test_medium/

%%bash dlem --output-tracks \ --plot \ --norm \ -l 1600 \ --device cpu \ -b ../tests/in_regions.bed \ GSE263229_GlambdaLmerged_fix.mcool \ ../tests/drosophila_test_medium/

In [4]:

from IPython.display import HTML, display
display(HTML(filename='../tests/drosophila_test_medium/in_vs_pred_chr3R_16527391_17055748.html'))

from IPython.display import HTML, display display(HTML(filename='../tests/drosophila_test_medium/in_vs_pred_chr3R_16527391_17055748.html'))

Run dLEM -- Large¶

All outputs, all chromosomes, even take down resolution 400 for testing

In [ ]:

%%bash

dlem --output-tracks \
    --output-cool \
    --plot \
    --norm \
    --all \
    -l 400 \
    --device cpu \
    -b ../tests/in_regions.bed \
    GSE263229_GlambdaLmerged_fix.mcool \
    ../tests/drosophila_test_large/

%%bash dlem --output-tracks \ --output-cool \ --plot \ --norm \ --all \ -l 400 \ --device cpu \ -b ../tests/in_regions.bed \ GSE263229_GlambdaLmerged_fix.mcool \ ../tests/drosophila_test_large/

In [7]:

from IPython.display import HTML, display
display(HTML(filename='../tests/drosophila_test_large/in_vs_pred_chr3R_6552201_7088853.html'))

from IPython.display import HTML, display display(HTML(filename='../tests/drosophila_test_large/in_vs_pred_chr3R_6552201_7088853.html'))