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.
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.
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.