xiekunwhy

Hi, Can I break genome sequences into small pieces (~ 10 M ) and use HiTE to annotate each piece independently, then combined results? Best, Kun

For such a heavy pipeline, I think that one-command design is not a good idea (including other similar pipeline like EDTA https://github.com/oushujun/EDTA , EarlGrey https://github.com/TobyBaril/EarlGrey , ltr_retriever (https://github.com/oushujun/LTR_retriever) , they...

I got the same error

Also want to know if SegmentNT can use for gene structure annotation, and how if it can.

This is https://anaconda.org/bioconda/spaln, but may be not work well ( the conda version of spaln on my computer is always segment fault).

Can I use basecall_model_version_id=dna_r9.4.1_e8_hac\@v3.3 as input data for --ont?

also hope some one can answer this question. And explain the expected the hap* size and the mixed (*.hic.p_ctg.fa) size.

I met the same problem. 3/4 genome met the same problem.

只有-v和-sf是输入文件，其他的都不是文件。-v输入的是保存变异信息的vcf；-b1是bulk1（野生/显性混池）在vcf中的名字，不是文件；-b2是bulk2（突变/隐性混池）在vcf中的名字，不是文件；类似的，-p1和-p2对应亲本1（与-b1的性状对应的）和亲本2（与-b2的性状对应的）在vcf中的id。

您是对bsa测序有什么误解吗，一组完整的bsa数据就4个样本，一个是p1，一个是p2，一个是bulk1的一个是bulk2的。不理解您说的多个系是什么，如果有多个混池一起放在一个vcf里，也不影响4个样本的组合。