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Could you please explain a bit in detail what is expected as input by the scriptALLHiC/scripts/link_superscaffold.pl
Thanks
Diego
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Hi,
I got two phenomena when using Canu and hope you guys could help me solve the problems. It's about different Canu versions and different PacBio sequencing methods.
The first is when I using PacB…
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Dear Xingtan,
After I ran Pilon for error correction, I found some error like this.
Look like allhic extraction cannot read my fasta length. Do you have any solutions?
), which is an allopolyp…
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Dear Dr. Zhang,
This is Xiaofei Yang, from Xi'an Jiaotong University. Thanks for your tool ALLHiC, first.
I try to use it to correct our draft assembly. We have sequenced hic of six libraries, sho…
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Hi @tangerzhang ,
I am working on a highly heterozygous diploid genome. We used long reads in the assembly. The assembly reference has been corrected for miss assemblies. We mapped the HiC reads an…
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Hi, I am running ALLHiC on a polyploid genome. Everything went fine till at the rescue stage a few perl messages like these showed up:
Number of original contigs in contig000650: 0
Number of resc…
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Thank you for the algorithm！
But when I scaffoldof a simple diploid genome(1n = 2x = 16) with K value =8 , one of clusters were much bigger than the others.
How to determine K value for diploid？
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Hi,
Hi,
Iam currently using ALLHiC on a diploid draft assembly. I have a two questions though:
1) The number of pre defined groups (k) in the ALLHiC partition is the same as the number of chrom…
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Hi @tangerzhang ,
I have a high heterozygosity polypoidy genome to assembly. After reading the manusrcript of ALLHiC and issues in the github, I want to confirm the typical workflow for ALLHiC scaf…
baozg updated
5 years ago