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Hi Gavin
I've been running the Titan snakemake workflow and would be grateful if you could clarify a few things for me:
1. In the optimalClusterSolution.txt file, what does the "...cluster_X_" a…
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Hi @AntonBankevich ?
Is there need to purge haplotype duplication of the output assebmly ?
As far as I know, Canu and HiFiasm needs another run of purge_dups.
Thanks in advance!
Sincerely
…
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Hi,
This is my first time using QUILT, I am trying to impute genotypes in the location of ~300 SNVs.
Preprocessing of the bam files I used included alignment to GRCh38 with BWA, marking and rem…
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Hi
Thanks for developing this tool.
I now have resequencing data for two parents: **P19_clean_1.fq.gz,P19_clean_2.fq.gz,P48_clean_1.fq.gz,P48_clean_2.fq.gz**, and the offspring ONT (R10.4.1) data: *…
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Hi there
I'm trying to phase a hexaploid plant genome showing a haploid length of ~1,6Gb
A total of six sequel II SMRT cells were mapped into a haploid version of this genome generated with hifasm…
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Hi, `WhatsHap` developer! I was going to use `WhatsHap` subcommand `whatshap compare` to calculate the **Switches** and **Flips** between **Truth** and **Query**, but I was still confused with the det…
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The VCF spec contains this text on ALTs:
> Options are base Strings made up of the bases A,C,G,T,N,\*, (case insensitive)
or an angle-bracketed ID String (“\”) or a breakend replacement string as …
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Hi,
I'm new to diploid assemblies and have a few questions about what the different output files represent.
I have a flye assembly with 233 contigs.
After hapdup i have two dual assemblies, one …
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Hi,
I use the freebayes to call SNPs and InDels in polypoidy genotype from HiFi aligned bam (120x for haploid genome). And also have the Ultra-long reads aligned bam (reads N50 50kb) 60x. But the b…
baozg updated
3 years ago
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孙老师您好！我有几个疑问.
1. 首先只用一个物种T. sinense(tsi)得到了第一个祖先核型即AEK, 植物存在WGD, 所以一堆WGD产生的染色体选一条即可.
2. 但如果是不存在WGD的动物, 原始的lens.file就等于老师用到的aek_tsi13s.txt(WGD产生的多条同源染色体中选一条)吗？
3. 再接着运行-d -icl -bi -c -km, …