FR: Return NFR-, mono-, di-, and tri-nucleosome signal tracks

[ccrobertson]

Thank you for this great tool! In addition to the inferred states, we are interested in using the signal tracks that HMMRATAC uses as input to the HMM algorithm for some analyses. Is there a way to output these when running the program?

I see in your code there is an option --printHMMRtracks. We tried using this option and expected it to return signal tracks as *_nfr.bedgraph, *_mono.bedgraph, *_di.bedgraph, and *_tri.bedgraph files. But when we ran this, no additional files were returned as compared to running without the --printHMMRtracks option.

Thanks for any help!

[Mikxox]

As you can see in src/java/HMMR_ATAC/MAIN_HMMR_Driver line 134 // printHMMRTracks = p.getPrintHMMRTracks(); , the printing option is currently commented out, you would have to manually undo this in the code by either re-adding it, or simply setting it to true via printHMMRTracks = true;.

Furthermore there is a coding mistake in src/java/HMMR_ATAC/HMMRTracksToBedgraph in the run() function, making the generated files still simply be empty files. To fix this, the run function should be changed to

	private void run(){
		this.nfr = new ArrayList<>();
		this.mono = new ArrayList<>();
		this.di = new ArrayList<>();
		this.tri = new ArrayList<>();

		this.nfr.addAll(runOneCol(0));
		this.mono.addAll(runOneCol(1));
		this.di.addAll(runOneCol(2));
		this.tri.addAll(runOneCol(3));
	}

If you make both these code edits and rebuild the jar, you should get the output files you're asking for.

[ccrobertson]

Thanks so much for the help! We did previously try uncommenting that line in the code, but did not make any changes to the run() function. Will give this a try now! Thanks again

[sunmeilin2]

I git clone https://github.com/LiuLabUB/HMMRATAC,and make both these code edits but don't know how to rebuild the jar,could you offer me some advice?
Thank you foy your help!

[Mikxox]

I git clone https://github.com/LiuLabUB/HMMRATAC,and make both these code edits but don't know how to rebuild the jar,could you offer me some advice? Thank you foy your help!

I would recommend simply using https://github.com/Mikxox/HMMRATAC

[sunmeilin2]

Hi,Mikxox,I just wonder how I install this version of HMMRATAC ,I install the liulab-HMMRATAC with conda,but it seems that this version is not in the conda list
Best
meilin

[Mikxox]

Hi,Mikxox,I just wonder how I install this version of HMMRATAC ,I install the liulab-HMMRATAC with conda,but it seems that this version is not in the conda list Best meilin

In your conda environment you will find a folder hmmratac-1.2.10 and inside will be another folder /share inside that folder simply replace the HMMRATAC.jar file with the new .jar file and rename it to the exact same name the original had. That should be all that is needed.