Which file is the final output file of matrix2EigenVectors.py？

[kuangzhuoran]

Hi !
my command is

1. python2 runchangematrix.insulation.py -i Chr1_dense.matrix -g sp1 -c Chr1 -o runchangematrix -s 40000
2. perl matrix2compartment.pl -i runchangematrix/sp1_Chr1_40000.insulation.matrix -o matrix2compartment/Chr1 --et
3. python2 matrix2EigenVectors.py -i Chr1.zScore.matrix.gz -r sp1.gene.gff -v

Then I got 3 output files：
Chr1.zScore.compartments.refSeq.txt
Chr1.zScore.compartments
Chr1.zScore.eigen1.bedGraph

I found that the output of the 3 output files is not identical
Chr1.zScore.compartments.refSeq.txt gives the opposite result to the other two

[kuangzhuoran]

I think Chr1.zScore.compartments.refSeq.txt should prevail

Because I also tried the Juicer Eigenvector, and calculated the correlation between the PC1 values given by Juicer and the GC content and gene density, the results were the same as Chr1.zScore.compartments.refSeq.txt

[kuangzhuoran]

Sorry I got it wrong, I rechecked the correlation between PC1 values and GC content.
Chr1.zScore.compartments and Chr1.zScore.eigen1.bedGraph to get the right result

and the Chr1.zScore.eigen1.bedGraph in the log file was generated last