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Hi, @tanghaibao and @tangerzhang ,
From discriptions, i found this pipelines work well, and I am wondering if this process can be applied to diploid plants. if it is possible, can you give me some …
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Hello,
Thank you so much to design such an excellent software to do with HiC assembly! I am a green hand in genome assembly. Now I am going to generate the Allele.ctg.table, but I am confused of th…
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Hi,
I was wondering if this tool produces the full length haplotypes with the common reagon in each fasta file produced or it just gives the fasta for sequences that are uncommon between the haplotyp…
bd904 updated
5 years ago
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hi,
I am very interested in algorithm details about the ordering and orientations for contigs. However the allhic is a binary code script. I want to get the readable code detail of the binary softwa…
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Hi there,
I got a run time error from building fasta step, details are below:
```
12:06:45 getFastaSizes | NOTICE Parse FASTA file `MR_H.fasta`
12:06:48 mergeTours | NOTICE Import `REduced.p…
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I used two draft genome to conduct the command "blastn" and "blastn_parse.pl", and two *.blast.out files were generated. When then command "classify.pl", the three files were none, including Allele.…
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Hi, @tanghaibao and @tangerzhang ,
Compared to the reference genome, I found many inversions and other structural errors in the allhic results. I wanted to know if there were any post scripts in yo…
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Hi, I am assembled a high heterozygous genome. The assembled size is larger than estimated size. Do I need to remove the alternative contigs before using AllHic?
Thanks for any advices~
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Hi @tanghaibao and @tangerzhang ,
I am working on denovo plant genome and I can't create `Allele.ctg.table`. In this case would the following work be correct?
```
PreprocessSAMs.pl sample.bwa_aln…
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gcc -Wall -I/public1/home/zhangxt/include -I. -Ihtslib-1.9 -c -o main.o main.c
In file included from main.c:33:
bcftools.h:42:50: error: expected ‘,’ or ‘;’ before ‘HTS_FORMAT’
void error(const …