nchernia
nchernia
The mega.sh script uses the flags -g and -s. For juicer I use -z and -y , but these flags do not work with the mega.sh script. So I used...
In my ideal world, we would restructure Juicer to be a set of cluster-specific scripts (the juicer.sh) together with a folder common/ that contained scripts that are the same across...
Hello, I was wondering if there could be an option to stream cytosine_report instead of writing it to an output file. It's pretty big (28G) and I only keep it...
**Describe the bug** Dump gives an error when there shouldn't be. Difference between jar 1.19 and 1.22 **To Reproduce** java -jar juicer_tools_1.19.02.jar dump observed KR https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3262nnn/GSM3262956/suppl/GSM3262956_D00_HiC_Rep1.hic chr1 chr1 BP 5000...
E.g. hg19 chr1 at 50Kb, there's a bin at the end; we should not output this since it leads to problem when converting to wig/bigWig. Should also make an option...
When loading tracks it's okay to have a null genome but we throw an error. This happens e.g. if people are using custom genomes and then trying to load tracks....
We should use sumCounts instead of the 2.5Mb diagonal to determine if there are enough Hi-C contacts to run HiCCUPS / Arrowhead
The statistics should be calculated within the jar. If a restriction site file is sent in, we will calculate those statistics as well. By default we will not include statistics...
The default should be that intra fragment reads are kept, and there should be a flag for getting rid of them.