ALLHiC

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partition.pl vs partition_gmap.pl vs partition_gmap.py

1

Dear @tangerzhang and @tanghaibao, I see some inconsistencies between the files partition.pl vs partition_gmap.pl vs partition_gmap.py. I would like to know whether this is intended or whether it is an...

diriano

Hi I´m trying to solve the chromosomes of a fungal specie (haploid). I successfully ran the correction steps. When I try to run the partition step, I have an error...

Karina-atriztan

Why there is only one group?

4

Hi @tangerzhang After parition, there is only one group. This is my code ``` parallel -N2 -k -j 4 "bwa-mem2.avx512bw mem -R '@RG\tID:{1}\tPL:illumina\tSM:{1}' -t 8 ${r} {1} {2} | samtools...

Johnsonzcode

empty plot

6

老师您好， 在运行ALLhic对简单基因组进行挂载时，日志似乎表示运行成功，也出现了最后的结果，挂载率也能到90%以上。但绘图时热图却是空白的。简单测试好像是互作矩阵计算为0。请问是什么原因造成这种问题。 谢谢老师！ 

GaoChengyu

Hi, @tangerzhang, sorry to disturb you again. After checking the file according to the instruction in #150, my files look like the same as required, but my plot is still...

Huangxc01

gmap2AlleleTable.pl error: Use of uninitialized value $gene in substitution (s///) at gmap2AlleleTable.pl line 20

2

Hi, @tangerzhang , sorry for disturb you. When I want to use gmap2AlleleTable.pl to aquire the Allelic.contig.table I encountered an error as below: [Use of uninitialized value $gene in substitution...

Huangxc01

allhic_partition

1

Hi Dr. zhang when I use the ALLHiC_partition，I maked k 29, but I total get 23 prunning.counts_GATC.29, Is this normal?

wyl1219

Dear @tangerzhang , my HiC data was digested with three different REs, how can I tell this to AllHiC? Thanks, Diego

diriano

Hi @jinxin112233 A1: You can use bwa mem and samtools sort to generate the sorted bam file. A2: ```seq.fasta``` is the draft contig file that was assembled by PacBio/Nanopore assemblers....

lilyynu

miniprot seems good to use. https://github.com/lh3/miniprot

wyim-pgl