Enhancer "signal" value

[MoHallal]

Hello, I have data generated from RNA-seq, ATAC-seq and H3K27ac ChIP-seq assays for the same mouse tissue and would like to try EAGLE to link putative enhancers to target genes. In the Usage you mention that enhancer "signal" value is required -E: A tab-delineate file indicate the enhancer positions and signals with format as "\t\t\t" From the paper on EAGLE model you mentioned that "We used the score for the enhancer annotation as a proxy of enhancer activity." and that "The enhancer annotation was obtained from our previous work, in which we integrated multiple genomic datasets to derive a set of reliable enhancer annotation in different tissue/cell types Can you please advise what is the signal that I should be using to test your model using my data? could it be the normalized read counts for the H3K27ac peaks for example? Thank you

[MoHallal]

Hello, One more thing :) I tired to run the example you provided and got the following error :

`perl EAGLE.pl -E inputexample/cell_enh.bed -G inputexample/cell_gene.txt  
-normalizing the input enhancers......
-Extracting the 100 Mb regions upstream/downstream TSS of the input genes......
-Calculating the correlations of input enhancers and genes......
-Setting the feature: Gene Scores......
-Setting the feature: Distances between enhancer and gene......
-Setting the feature: Enhancer Window Signals......
-Setting the feature: Gene Window Signals......
-Setting the feature: Weights of Enhancer-Enhancer Correlations......
-Combining all the features......
Running the final predictor......
MATLAB is selecting SOFTWARE OPENGL rendering.

                                                                                          < M A T L A B (R) >
                                                                                Copyright 1984-2020 The MathWorks, Inc.
                                                                            R2020b Update 4 (9.9.0.1570001) 64-bit (glnxa64)
                                                                                            January 7, 2021

Warning: Unrecognized command line option: minimize. 

To get started, type doc.
For product information, visit www.mathworks.com.

Error using horzcat
Dimensions of arrays being concatenated are not consistent.

Error in predictor (line 5)
Alldata=[candidatedata{2:7}];
`

Kindly note that I am using matlab R2020b and not the R2017b. Thanks!

[slives-lab]

I'm also encountering the same issue, using Matlab 2019a.

perl EAGLE.pl -E inputexample/cell_enh.bed -G inputexample/cell_gene.txt -S human -normalizing the input enhancers...... -Extracting the 100 Mb regions upstream/downstream TSS of the input genes...... -Calculating the correlations of input enhancers and genes...... -Setting the feature: Gene Scores...... -Setting the feature: Distances between enhancer and gene...... -Setting the feature: Enhancer Window Signals...... -Setting the feature: Gene Window Signals...... -Setting the feature: Weights of Enhancer-Enhancer Correlations...... -Combining all the features...... Running the final predictor...... MATLAB is selecting SOFTWARE OPENGL rendering.

                                                                                                    < M A T L A B (R) >
                                                                                          Copyright 1984-2019 The MathWorks, Inc.
                                                                                          R2019a (9.6.0.1072779) 64-bit (glnxa64)
                                                                                                       March 8, 2019

Warning: Unrecognized command line option: minimize.

To get started, type doc. For product information, visit www.mathworks.com.

Error using horzcat Dimensions of arrays being concatenated are not consistent.

Error in predictor (line 5) Alldata=[candidatedata{2:7}];