hic file, are the one used by HiC-Pro and described in the chrom.size file. It ensures that the chromosome names that you have in your. That's why now, the hicpro2juicebox.sh utils uses the HiC-pro annotation (-g chromosome_size) option. I guess they are not using the same annotation (Ensembl or NCBI) for all genome. ![]() However, we realized a few months ago that according to the genome, the chromosome names used by Juicebox are not the same. In this case, it will use its own annotation file. hic file, you can specify the organism to Juicebox (hg19, mm9, etc.). >head test_results/hic_results/data/dixon_2M/dixon_2M_allValidPairs * In the same way, which version of HiC-Pro are you using ? could you check wether you have all the require field in the allValipPairs file ? ie. * Which version of the hicpro2juicebox.sh are you using ? It would be nice to regenerate the hic file with the last version. * You should also try the exemple in their website. I would suggest to reinstall the ctl part. * Juicebox and the command line tools can be independantly installed. Well, here it failed but this is just because my test data are too small. HiC contact map is too sparse to run Arrowhead, exiting. >java -jar /bioinfo/local/build/juicebox/juicebox_clt_1.4.jarÄump observed NONE. ![]() ~/Apps/HiC-Pro_2.7.9/annotation/HindIII_resfrag_hg19.bed bioinfo/local/build/juicebox/juicebox_clt_1.4.jar -r >~/Apps/HiC-Pro_2.7.9/bin/utils/hicpro2juicebox.sh -i test_results/hic_results/data/dixon_2M/dixon_2M_allValidPairs
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