aidenlab juicer issues - Githubissues

aidenlab / juicer

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

http://aidenlab.org

MIT License

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issues

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How can I generate a .hic contact matrix at the fragment level using Micro-C data?

#359 hanshanmengqi opened 2 days ago
0
syntax error near unexpected token

#358 xingguowu closed 1 week ago
0
addnorm: Requested array size exceeds VM limit

#357 jiangshan529 opened 2 weeks ago
0
too slow to do full genome assemble

#356 dupuquan opened 2 months ago
0
NumberFormatException

#355 yuchun2323 opened 2 months ago
0
Too slow to get the inter.hic

#354 YouxinZhao opened 2 months ago
1
chimeric_sam.awk

#353 xueqinerer opened 2 months ago
0
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 3 months ago
1
Modify the chromosome number in the.hIC file

#351 shenlinyong opened 4 months ago
0
Form a combined .hic file

#350 narzouni opened 4 months ago
0
Provision of enzymes

#349 molinfzl opened 5 months ago
0
Treat hap1 and hap2 to as "parents" for diploid.sh

#348 sarjopp opened 6 months ago
0
Not able to see the specified normalizations (using -k) in the hic file after juicertools pre

#347 ashishjain1988 opened 6 months ago
0
Juicer changes chromosome names

#346 jeramiahsmith opened 7 months ago
1
Sorted file and dups/no dups files do not add up in dedup step

#345 WeiCSong opened 7 months ago
1
Trio-binning genome assembly and juicer error

#344 Larkinhi opened 7 months ago
0
samtools sort: fail to open "./samtools.36604.8950.tmp.1019.bam": Too many open files

#343 sanjin725 opened 7 months ago
3
Fixed queue time to use $queue_time

#342 emwjacobson opened 7 months ago
0
insufficient memory for the Java Runtime Environment - CPU

#341 james-vincent opened 8 months ago
1
.hic file chr names NC_000001.11

#340 Luzmist opened 8 months ago
0
Matrix size

#339 tan5251 closed 8 months ago
0
strange output of merged1.txt

#338 woodoo46 closed 8 months ago
0
error with Java when generating out_JBAT.assembly following Yahs protocol (Yet another HIC scaffolding tool)

#337 palasities opened 10 months ago
0
juicebox format to fasta: coordinates conversion error

#336 brysonab closed 11 months ago
1
Error while Normalizations

#335 Kaustav-93 opened 1 year ago
1
Installation files absent

#334 HaikuoLi opened 1 year ago
1
Juicer memory usage

#333 Xinxin0314 opened 1 year ago
0
More restriction enzyme sites of Arima than Juicer provided, how to modified juicer.sh

#332 QianghuiZhu opened 1 year ago
4
The sample data link in the wiki docs are no longer accessible

#331 jprorama opened 1 year ago
0
***! Error! Either inter.hic or inter_30.hic were not created

#330 yuntan1992 opened 1 year ago
5
Java memory error

#329 hwamu opened 1 year ago
0
awk error

#328 ratheraarif opened 1 year ago
0
After manual correction of juicebox convert to fasta

#327 ABDULLAHGUJJAR opened 1 year ago
0
sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

#326 MovmntR opened 1 year ago
1
GPU/CUDA Installation Not Detected

#325 tarak77 opened 1 year ago
3
Calculating norms for zoom BP_100000java.lang.ArrayIndexOutOfBoundsException: 1296

#324 maize821 opened 1 year ago
1
> Unknown command: statistics

#323 qdu-beep opened 1 year ago
1
awk: fatal: cannot open file /splits/hic.fastq.gz_norm.txt' for reading (No such file or directory)

#322 fengyuanli304 opened 1 year ago
0
Is it possible to calculate interchromosomal interactions using juicer?

#321 rahulk87 opened 1 year ago
1
Same chromosome, same hic-data, different scaffolding results

#320 anxuan-web opened 1 year 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 1 year ago
3
Clarify wiki

#318 imanmousaei opened 1 year ago
0
How to modify the juicer.sh script

#317 jacolmen opened 1 year 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