aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

http://aidenlab.org

aidenlab/juicer Issues

***! Error! Either inter.hic or inter_30.hic were not created
Updated 2 months ago5
Modify the chromosome number in the.hIC file
Updated 2 months ago
Form a combined .hic file
Updated 2 months ago
Provision of enzymes
Updated 2 months ago
> Unknown command: statistics
Updated 3 months ago1
insufficient memory for the Java Runtime Environment - CPU
Updated 3 months ago1
Sorted file and dups/no dups files do not add up in dedup step
Updated 3 months ago1
samtools sort: fail to open "./samtools.36604.8950.tmp.1019.bam": Too many open files
Updated 3 months ago2
Treat hap1 and hap2 to as "parents" for diploid.sh
Updated 4 months ago
Not able to see the specified normalizations (using -k) in the hic file after juicertools pre
Updated 4 months ago
Juicer changes chromosome names
Updated 4 months ago1
Error while Normalizations
Updated 5 months ago1
Trio-binning genome assembly and juicer error
Updated 5 months ago
GPU/CUDA Installation Not Detected
Updated 5 months ago2
strange output of merged1.txt
Closed 6 months ago
.hic file chr names NC_000001.11
Updated 6 months ago
Matrix size
Closed 6 months ago
Installation files absent
Updated 6 months ago1
More restriction enzyme sites of Arima than Juicer provided, how to modified juicer.sh
Updated 7 months ago4
error with Java when generating out_JBAT.assembly following Yahs protocol (Yet another HIC scaffolding tool)
Updated 8 months ago
Error running hiccupsdiff
Updated 8 months ago11
juicebox format to fasta: coordinates conversion error
Closed 8 months ago1
Error! The number of reads in the fastqs is not the same as the number of reads reported in the stats (0)
Updated 9 months ago1
Juicer memory usage
Updated 10 months ago
The sample data link in the wiki docs are no longer accessible
Updated 10 months ago
Java memory error
Updated 10 months ago
awk error
Updated 10 months ago
After manual correction of juicebox convert to fasta
Updated 10 months ago
sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Updated a year ago
Calculating norms for zoom BP_100000java.lang.ArrayIndexOutOfBoundsException: 1296
Updated a year ago1
Is it possible to calculate interchromosomal interactions using juicer?
Updated a year ago1
awk: fatal: cannot open file /splits/hic.fastq.gz_norm.txt' for reading (No such file or directory)
Updated a year ago
Same chromosome, same hic-data, different scaffolding results
Updated a year ago
Can I generate an asymmetric .hic file for an asymmetric matrix, and to illustrate the unsymmetric matrix by JuiceBox?
Closed a year ago3
Clarify wiki
Updated a year ago
How to modify the juicer.sh script
Updated a year ago2
gzip too slow
Updated a year ago
GPU for HiCCUPS - Cuda 12.0
Updated a year ago1
positive or negative signs of eigenvector
Closed a year ago1
juicer-v1.5.6, Problem with creating fragment-delimited maps, NullPointerException.
Updated a year ago
the genome was 25Gb and the use the juicerbox to modified the hic heatmap but its worng
Updated a year ago2
ava.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.
Updated a year ago
Please include example of pre command in various formats
Closed a year ago
juicer_tools pre produces empty heatmap
Updated a year ago
Is it possible for juicer using Bowtie2 to map reads instead of bwa ?
Updated a year ago
Why does not run with res: 40000 to produce results
Closed a year ago1
how to get sparse matrix for all chromosomes using juicer dump
Closed a year ago1
sort: write failed: /home/sdc/3ddna/HIC_tmp/sorty4gvbq: Input/output error
Updated 2 years ago
Calulate_map_resolution.sh issue
Updated 2 years ago7
empty heatmap
Closed 2 years ago