Cannot visualize hitile files

[rahmas36]

Hi, a colleague of mine performed a differential compartment analysis between a CRISPRi and scrambled control experiment using dcHiC. He provided me with a bedgraph file for the full compartment details and a bedgraph file for the differential compartments. The bedgraph files contain compartment information for the CRISPRi and scrambled samples. I attached a screenshot from the bedgraph file containing full compartment details. I used clodius to aggregate the bedgraph file into a hitile file so that it could be ingested into HiGlass. I did this individually for the CRISPRi experiment column (CNTNAP2(which is the gene inactivated by CRISPRi) and the scrambled column.

I ran clodius as so:

clodius aggregate bedgraph \ filename.bedGraph \ --output-file filename.hitile \ --chromosome-col 1 \ --from-pos-col 2 \ --to-pos-col 3 \ --value-col 4 (for CNTNAP2) or --value-col 5 (for Scramble) \ --assembly hg38 \ --has-header

Basically I wanted to generate hitile files for the compartment tracks from the experiment and the scrambled control to see if there is a compartment switch at the CNTNAP2 locus upon CRISPR inactivation of the gene. After I ingested the hitile files into HiGlass I could not visualize them. There was an error in retrieving the tileset. I attached the screenshot. When I was running clodius aggregate my computer froze, so I was unsure if the process was completed. When I restarted the computer, I could see that the hitile files were generated (2.2 MB each, and the bedGraph file is 3.5 MB), so I assumed that the aggregation worked.

I had previously aggregated bedGraph files of TAD insulation scores and was able to visualize on HiGlass. Not sure what went wrong with these new files. Any advice would be appreciated.

[pkerpedjiev]

Hi, any chance you could try converting the bedgraph to a bigwig file? Our support for hitile is patchy at best.