nservant
commented
6 years ago That's a good point, but I never tested arrowhead myself. I do not really see why it should come from the .hic file generated from HiC-Pro. If you can read it into Juicebox, I guess the file is OK.
In the past, I had some troubles with the annotation used in .hic format. Did you check that your Project/AT/Interaction/QC/AT.fa.len contains a "Chr1" chromosome ? and that there is no differences in chromosome names ? Otherwise, I would suggest to contact the arrawhead developper instead. If there is something to add in the .hic file, please let me know. best N
First, convert valid file to .hic file: sh HiC-Pro_2.10.0/bin/utils/hicpro2juicebox.sh -i ../../test -g Project/AT/Interaction/QC/AT.fa.len -j HiC-Pro_2.10.0/bin/utils/juicer_tools.1.7.6_jcuda.0.8.jar -o ./ -b 5000 Generating Juicebox input files ... Running Juicebox ... /share/nas2/genome/biosoft/java/jdk/1.8.0_31/bin/java -jar HiC-Pro_2.10.0/bin/utils/juicer_tools.1.7.6_jcuda.0.8.jar pre -r 5000 ./tmp/28805_allValidPairs.pre_juicebox_sorted .//test.hic Project/AT/Interaction/QC/AT.fa.len Not including fragment map Start preprocess Writing header Writing body ................ Writing footer
Finished preprocess
Calculating norms for zoom BP_5000 Writing expected Writing norms Finished writing norms done ! second, call TAD use arrowhead: /share/nas2/genome/biosoft/java/jdk/1.8.0_31/bin/java -jar juicer_tools_linux_0.8.jar arrowhead -c Chr1 -r 5000 test.hic xx Reading file: test.hic HiC file version: 8 Unable to assess map sparsity; continuing with HiCCUPS 100% 0 domains written to file: Project/AT/Interaction/Juice/REsults/xx/5000_blocks Arrowhead complete
No domain was predicted. Could you help to me ?