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Hi,
I skip the prunning part and when i use this command: ALLHiC_partition -b sample.clean.bam -r draft.asm.fasta -e GATC -k 9
the result give me 235 groups. I only set up 9 groups ,why it give me s…
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Hi,
I followed the installation but when I tried to run `ALLHiC_prune -h` I got the following error..
### ALLHiC_prune: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ALLHiC_…
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Hi, Zhang. I am trying to assemble haplotype genome using ALLHiC. I am puzzled by the partition.pl step using Allele.gene.table. And I find the alternative partition_gmap.py. So I have two questions:
…
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Hi @thackl
I am very interested in trying out your package (looks amazing!). However i am having trouble importing data:
> read_seqs(ex("emales/emales.fna"), parse_desc=FALSE)
Reading 'fasta' wi…
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Hi,
I'm running ALLHiC on an auto-tetraploid genome assembled with hifiasm. I firstly used ALLHiC_corrector to correct chimeric contigs and then used ALLHiC to scaffold them. But the results of eac…
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Hi Bao,
Thank you for sharing your nice codes!
I have a question about s1 population for Haplotype-aware Genetic Mapping.
Is there any reason why you chose S1 population? and can I use F1 populat…
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Hi, @tangerzhang
I'm trying to use ALLHiC to scaffolding an autopolyploid genome assembled using hifiasm. The coverage of my HiC data is ~150x. First, I used ALLHiC_corrector to correct chimeric co…
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Dear developers,
Thank for your software and careful manual. I just used ALLHiC to assemble haplotype genome with an allotetraploid geome from same species, and it worked fluently until I tried to …
wu116 updated
2 years ago
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Hi
I tried to use ALLHiC to scaffold my draft genome. The overall result looks good, but some contigs are mis-assembled ,because of lacking high-quality whole genome sequence of related species at pr…
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Hi, I got `panic: runtime error: index out of range` when I ran ALLHiC scripts `sh allhic_pbs.sh QMg_NbQ4P_RN.fasta 38 GATC`:
```
#!/bin/bash
#Usage: sh allhic_pbs.sh QMg_NbQ4P_RN.fasta 38 GATC
…