How to create the cell state name file, etc for creating giggle heatmap

[peveral...@gmail.com]

Hi Ryan,

I'm referring to the Example Analysis - Roadmap Epigenomics in your Github page.

In particular this section:

# Plot
sudo apt install python python-pip python-tk
pip install matplotlib
$GIGGLE_ROOT/scripts/giggle_heat_map.py \
 -s $GIGGLE_ROOT/examples/rme/states.txt \
 -c $GIGGLE_ROOT/examples/rme/EDACC_NAME.txt \
 -i GSM1218850_MB135DMMD.peak.q100.bed.gz.result \
 -o GSM1218850_MB135DMMD.peak.q100.bed.gz.result.3x11.pdf \
 -n $GIGGLE_ROOT/examples/rme/new_groups.txt \
 --x_size 3 \
 --y_size 11 \
 --stat combo \
 --ablines 15,26,31,43,52,60,72,82,87,89,93,101,103,116,120,122,127 \
 --state_names $GIGGLE_ROOT/examples/rme/short_states.txt \
 --group_names $GIGGLE_ROOT/examples/rme/new_groups_names.txt

My question are what are the rules for creating these files?

$GIGGLE_ROOT/examples/rme/states.txt
$GIGGLE_ROOT/examples/rme/EDACC_NAME.txt
$GIGGLE_ROOT/examples/rme/new_groups.txt
$GIGGLE_ROOT/examples/rme/short_states.txt
$GIGGLE_ROOT/examples/rme/new_groups_names.txt

  

i.e. the ordering of name, groups, how many rows,  etc.

Because  this giggle output file has no indication the column (state) information, e.g. TssA, TssAFlnk, etc.




GSM1218850_MB135DMMD.peak.q100.bed.gz.result




Moreover that result file has 1906 rows, where as $GIGGLE_ROOT/examples/rme/new_groups.txt has 127 rows.

Thanks and hope to hear from you again.




P.D.


[Ryan Layer]

$GIGGLE_ROOT/examples/rme/states.txt

column names

$GIGGLE_ROOT/examples/rme/EDACC_NAME.txt 

maps names to ID that is used in the original file name  

$GIGGLE_ROOT/examples/rme/new_groups.txt

A more set of names

$GIGGLE_ROOT/examples/rme/short_states.txt

shortened state names

$GIGGLE_ROOT/examples/rme/new_groups_names.txt

row names after clustering by group

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