error: unrecognized arguments: comp_signal hic_matrix_pca1.bedgraph

[yermekaitenov]

Hello,
I'm having an issue when trying to run a get_pentad_cis.py script.
It recognizes my .cool file, but not the bedgraph file with the first eigenvector (PCA1) of a Hi-C matrix.
Whereas it says "You could use the ‘::’ syntax to specify a column name from the bedGraph file", there are no headers in my file and it looks like this:
chr1 0 2000000 0.009910410970
chr1 2000000 4000000 -0.034634710334
chr1 4000000 6000000 -0.042192360907
...
How can I specify that column? Or could there be an issue with the titles where it should explicitly end with bedGraph (capital "G") and not bedgraph?
Many thanks.

[magnitov]

Hi @yermekaitenov ,

When developing the scripts, I was having in mind the structure of compartments file called by cooltools package.
The have bedGraph-like structure, that has same columns as you have, but with a header line. To make scripts work, you just have to add titles to the file you have in any text editor:

chrom start end SAMPLE_NAME
chr1 0 2000000 0.009910410970
chr1 2000000 4000000 -0.034634710334
chr1 4000000 6000000 -0.042192360907

Then specify the column with sample in the following manner: compartment_signal.txt::SAMPLE_NAME for comp_signal argument. See run_test.sh for more examples on how to run the scripts.

Best,
Mikhail