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aidenlab
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juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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Thanks - someone else noticed this too and made a pull request and I wrote there as well. See https://github.com/theaidenlab/juicer/pull/26
#352
Djangodu
opened
6 days ago
1
Modify the chromosome number in the.hIC file
#351
shenlinyong
opened
1 month ago
0
Form a combined .hic file
#350
narzouni
opened
1 month ago
0
Provision of enzymes
#349
molinfzl
opened
1 month ago
0
Treat hap1 and hap2 to as "parents" for diploid.sh
#348
sarjopp
opened
3 months ago
0
Not able to see the specified normalizations (using -k) in the hic file after juicertools pre
#347
ashishjain1988
opened
3 months ago
0
Juicer changes chromosome names
#346
jeramiahsmith
opened
4 months ago
1
Sorted file and dups/no dups files do not add up in dedup step
#345
WeiCSong
opened
4 months ago
1
Trio-binning genome assembly and juicer error
#344
Larkinhi
opened
4 months ago
0
samtools sort: fail to open "./samtools.36604.8950.tmp.1019.bam": Too many open files
#343
sanjin725
opened
4 months ago
2
Fixed queue time to use $queue_time
#342
emwjacobson
opened
4 months ago
0
insufficient memory for the Java Runtime Environment - CPU
#341
james-vincent
opened
5 months ago
1
.hic file chr names NC_000001.11
#340
Luzmist
opened
5 months ago
0
Matrix size
#339
tan5251
closed
5 months ago
0
strange output of merged1.txt
#338
woodoo46
closed
5 months ago
0
error with Java when generating out_JBAT.assembly following Yahs protocol (Yet another HIC scaffolding tool)
#337
palasities
opened
7 months ago
0
juicebox format to fasta: coordinates conversion error
#336
brysonab
closed
8 months ago
1
Error while Normalizations
#335
Kaustav-93
opened
9 months ago
1
Installation files absent
#334
HaikuoLi
opened
9 months ago
1
Juicer memory usage
#333
Xinxin0314
opened
9 months ago
0
More restriction enzyme sites of Arima than Juicer provided, how to modified juicer.sh
#332
QianghuiZhu
opened
9 months ago
4
The sample data link in the wiki docs are no longer accessible
#331
jprorama
opened
9 months ago
0
***! Error! Either inter.hic or inter_30.hic were not created
#330
yuntan1992
opened
9 months ago
5
Java memory error
#329
hwamu
opened
9 months ago
0
awk error
#328
ratheraarif
opened
9 months ago
0
After manual correction of juicebox convert to fasta
#327
ABDULLAHGUJJAR
opened
10 months ago
0
sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
#326
MovmntR
opened
10 months ago
0
GPU/CUDA Installation Not Detected
#325
tarak77
opened
10 months ago
2
Calculating norms for zoom BP_100000java.lang.ArrayIndexOutOfBoundsException: 1296
#324
maize821
opened
10 months ago
1
> Unknown command: statistics
#323
qdu-beep
opened
11 months ago
1
awk: fatal: cannot open file /splits/hic.fastq.gz_norm.txt' for reading (No such file or directory)
#322
fengyuanli304
opened
11 months ago
0
Is it possible to calculate interchromosomal interactions using juicer?
#321
rahulk87
opened
11 months ago
1
Same chromosome, same hic-data, different scaffolding results
#320
anxuan-web
opened
11 months ago
0
Can I generate an asymmetric .hic file for an asymmetric matrix, and to illustrate the unsymmetric matrix by JuiceBox?
#319
luoxun-xl
closed
11 months ago
3
Clarify wiki
#318
imanmousaei
opened
11 months ago
0
How to modify the juicer.sh script
#317
jacolmen
opened
12 months ago
2
gzip too slow
#316
JiantaoZhao426
opened
1 year ago
0
positive or negative signs of eigenvector
#315
mengwill
closed
1 year ago
1
juicer-v1.5.6, Problem with creating fragment-delimited maps, NullPointerException.
#314
XiaoyangDai1
opened
1 year ago
0
the genome was 25Gb and the use the juicerbox to modified the hic heatmap but its worng
#313
Jiangjiangzhang6
opened
1 year ago
2
Error running hiccupsdiff
#312
rahulk87
opened
1 year ago
11
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.
#311
molecule53
opened
1 year ago
0
Please include example of pre command in various formats
#310
DavidWarrenKatz
closed
1 year ago
0
Error! The number of reads in the fastqs is not the same as the number of reads reported in the stats (0)
#309
carrie1s
opened
1 year ago
1
juicer_tools pre produces empty heatmap
#308
molikd
opened
1 year ago
0
Is it possible for juicer using Bowtie2 to map reads instead of bwa ?
#307
AssumeAssume
opened
1 year ago
0
GPU for HiCCUPS - Cuda 12.0
#306
nponts
opened
1 year ago
1
Why does not run with res: 40000 to produce results
#305
songxh1996
closed
1 year ago
1
Update README
#304
nchernia
closed
1 year ago
0
how to get sparse matrix for all chromosomes using juicer dump
#303
jiangshan529
closed
1 year ago
1
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