ALLHiC

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some problems in "allhic alleles" command

1

Hi, @tanghaibao I'm trying to use "allhic alleles" to get "alleles.table" from "paf", but it generates nothing. so what should I do? the allhic version is 0.9.13 Thanks in advance...

socialhang

Issue about partition result

3

dear professor, I was assembling a triploid genome.The input of allhic is from hifiasm, `*.asm.p_utg.fa ` which is without "bubble". Runing the partition step, weird results were found. `ALLHiC_partition -b...

YuChrming

partition_gmap.py without bam but with fasta file

10

Dear Xingtan, When I use partition_gmap.py to separate chromosome group for fasta and BAM, some chromosomes didn't have any bam file but fasta file. Do you have any ideas for...

wyim-pgl

Hello, When drawing the heatmap by using ALLHiC_plot, how to add dotted line between the chromosomes in 'Whole_genome.pdf'? I tried it but failed. Best wishes. Thanks.

pxxiao-hz

overestimated Chromosome size.

2

Hi, Prof. Zhang, Recently, i have a dipolid geome (2n=12) project. And it has 1.7% heterozygosity. Fisrt, i removed redundant sequnces using purge_haplotigs. Then, these contigs were scaffolding using ALLHIC....

shehongbing

Allele.ctg.table does not eliminate any read in prune step

6

Dear developers of AllHiC Thanks a lot for having developed this software to solve the problem of scaffolding polyploid genomes resulting in false-positive contact information between closely related copies. For...

edanchin

Hello, I have a question about the input dataset when using ALLHIC. I've phased my target diploid genome assembly into contig-level using Falcon-Unzip and Falcon-Phase. Now, I want to scaffold...

minjeongjj

The revised Prune program need more libraries

2

After installing htslib by the server admin, now it needs another lib. Is there any way to know how many more libs it need. Also the new revised Prune is...

hamidashrafi

Intermediate files in size of Tb?

6

Hi @tangerzhang, I am running allhic with a genome of size around 3 Gb, at a read coverage of 100x. I observed super large sizes of intermediate files during pruning...

HeQSun

How to use HIC data in the hifiasm and allhic assembly strategies？

2

Hi, Thanks for developing this useful tool. I assembled two haplotypes from a diploid plant using the hifiasm tool with HiFi and HiC data. Now, I use HiC data to...

naturalstay