ALLHiC

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ALLHiC_corrector crashes

6

Hi, I am trying to run ALLHiC_corrector, but get the following error. DO you have any recommendations? [13:29:17] Contig: ptg000402l Getting mapping list [13:29:17] Contig: ptg001136l Getting mapping list Traceback...

HMPNK

Why the allhic results were not consistent with my genetic linkage map?

1

Hi， I use allhic to generate the seq.HiCcorrected.fasta, then I use my genetic linkage map to group contigs. Finally, I use allhic to generate the genome. The following image shows...

baishengjun

haplotype assembly for a polyploid

5

Hi, This follows the issue #80 The problem was the group assignment to the chromosomes homologous groups. We are working on the assembly of a tetraploid potato. If we do...

phrh

Died at partition.pl line 59

3

hi, when i run 'partition.pl -g Allele.gene.table -r draft.asm.fasta -b sample.clean.bam -d wrk_dir', the error is:Died at /data/software/ALLHiC/scripts/partition.pl line 59. Why is that？

Ahahaha3

How to improve grouping and scaffolding?

2

Hi I'm running AllHiC to phasing/scaffolding tetraploid potato genome, with draft assembly of 6692 contigs and 2.4 Gb length I run every step in the wiki tutorial for sugarcane, How...

ddelgadillod

Plotting stage

1

Hi At plotting stage, it is not clear how the chrn.list can be prepared, especially the length of each group. Could you please explain a bit more?

ardy20

final groups' lengths have a big difference

3

Hi dear senior, Thank to your excellent scripts I was able to obtain 9 groups of contigs, however, I found that group2 has a ultra big length while group9 is...

tinyfallen

IndexError: list index out of range

13

When I run "ALLHiC_plot sample.clean.bam groups.agp chrn.list 500k pdf", I met the mistake Traceback (most recent call last): File "/public/home/zbjia/soft/ALLHiC/bin/ALLHiC_plot", line 249, in read_count_per_chr, read_count_whole_genome = calc_read_count_per_bin(chr_len_db, chr_order, read_on_chr, bin_size)...

JiaZhibo123

Non model organism and trim reads ?

10

Hello, 1) I am working with a non model organism (a diploid insect), thus we don't have any Closely related 'diploid' species. Can I still use ALLHIC ? 2) My...

ptranvan

ALLHiC optimize可以跳过GA吗

2

我在使用ALLHiC组装简单的二倍体时发现，optimize这一步可能会将原来正确的朝向搞错 这是使用optimize默认参数绘制的热图  根据信号强弱变化，左下角的方向可能是反了  于是我试着optimize 用 --skipGA跳过GA步骤结果绘制的热图  结果可能更加符合预期 我想问的是 1. GA步骤是如何根据clm文件确定contig的朝向呢？ 2 GA步骤是否是必须的？

xuzhougeng