zengxiaofei HapHiC issues

zengxiaofei / HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

https://www.nature.com/articles/s41477-024-01755-3

BSD 3-Clause "New" or "Revised" License

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issues

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I may have encountered some bugs due to the python version

#41 Weihankk closed 3 months ago
3
Unable to install due to Intel channel issues

#40 ChuanzhengWei closed 3 months ago
10
alternatives to Intel channel?

#38 DiegoSafian closed 3 months ago
4
The maximum number of clusters is even less than the expected number of chromosomes.

#37 sip123a closed 3 months ago
7
Issue of generate the final FASTA file after manual curation in Juicebox

#36 haoran-chn closed 4 months ago
7
the final number of groups was smaller than the nchrs I set.

#35 YanChunL closed 4 months ago
5
Is it normal for there to be interactions between haps?

#34 zoumingr closed 4 months ago
6
Parameter for output directory

#33 tbenavi1 closed 4 months ago
3
Important: More information allows me to grasp your issue faster

#32 zengxiaofei opened 5 months ago
0
Why is there only one cluster in the HapHiC_cluster.log

#31 zhangmeng123456abc closed 4 months ago
3
How to improve the haphic result for polyploid?

#30 vergilback closed 4 months ago
7
Each group only contains one contig

#29 YanChunL closed 5 months ago
11
How to set the chromosome number if I use p_ctg.fa from hifiasm when running haphic pipeline

#28 utpala101 closed 4 months ago
8
Failed to use haphic.

#27 ZJin2021 closed 6 months ago
2
BED file support

#26 amvarani opened 6 months ago
3
high number of chromosomes not accepted?

#25 Rhia15 closed 6 months ago
3
How to correctly reassignment？

#24 zjygoo closed 5 months ago
4
Unexpected keyword argument 'affinity'

#23 kokyriakidis closed 6 months ago
4
How to improve allotetraploid scaffolding in haphic?

#22 RezwanCAAS closed 5 months ago
13
Work with hifiasm using haplotype-specific data

#21 chenzixi07 closed 6 months ago
11
How to add/remove elements to a haphic plot?

#20 zhengyanstu closed 6 months ago
3
How to define the nchr for the pipeline

#19 chenzixi07 closed 7 months ago
2
N region in plot

#18 xiekunwhy closed 8 months ago
8
Question regarding Trio Binning files

#17 carolhsb closed 8 months ago
2
Correct way to run HapHiC with Hifiasm (HiC) data

#16 RunpengLuo closed 8 months ago
2
correct and Clustering

#15 ErickTong closed 7 months ago
6
The question about regenerating a HiC contact map for the final assembly

#14 qdu-beep closed 8 months ago
2
Error: died with <Signals.SIGKILL: 9

#13 Zhenlisme closed 8 months ago
4
ModuleNotFoundError: No module named 'pysam'

#12 chenHuiRu8 closed 8 months ago
1
Overrepresented / duplicated contigs as input

#11 jolbi closed 8 months ago
1
Omni-C support ?

#10 amvarani closed 9 months ago
3
How does HapHiC process collapsed contigs?

#9 Iven-gif closed 9 months ago
3
absence of correlation between HiC contacts and generated assembly file for manual curation

#8 dabitz closed 9 months ago
5
TypeError: object of type 'NoneType' has no len()

#7 yt619 closed 9 months ago
5
haphic plot

#6 YaoZhou89 closed 11 months ago
5
pore-C data

#5 socialhang closed 4 months ago
26
scikit-learn error, ImportError: dlopen: cannot load any more object with static TLS

#4 Boer223 closed 11 months ago
5
Juicerbox YaHS

#3 tianjio closed 9 months ago
1
Perform not so good for haplotype mixed assembly

#2 xiekunwhy closed 6 months ago
25
Number of chromosmes if using two pseudo haplotypes from hifiasm

#1 chregu1971 closed 11 months ago
1