Hanjiangna

Dear 3D-DNA developers, I have noticed that during the correction phase of the 3D-DNA pipeline, certain telomeric segments of contigs are sometimes trimmed. This appears to occur due to the...

Unexpected Zero Reads Pairs and Output Size with yahs and Juicer Preprocessing Pipeline

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Hello Developers, I have been utilizing yahs for Hi-C data processing followed by Juicer's preprocessing pipeline. My command for running yahs was: ```bash yahs /NGS/Fungi/Rc/juicer/references/R0301HifiHicOnt.asm.hic.hap2.p_ctg.fa R0301onthap2.sort.bam -e GATC ``` During...

Does CBNplot Discretize Input VSD Data During Network Construction?

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Hello developers and users, I am deeply intrigued by the process CBNplot employs to construct Bayesian Networks and I am particularly interested in understanding how it handles continuous data. Specifically,...

Hello I'm currently assembling a diploid fungal genome using hifiasm and Hi-C ont hifi data. After analyzing the data with juicer and applying 3d-dna, I've discerned the structure of two...

Dear developer Error reading from the FASTA/Q stream. Minimum return code for left and right read was (-2). code salmon quant -i $IndexDir -p 15 -l A -1 ${CleanDataDir}/${treat}${CleanReads1Suffix} -2...

有个真菌杂合二倍体，现在用hifiasm 组装获得了两个单倍型contig级别基因组，现在把hap1和hap2合并，跑all-hic 挂载，想看下hifiasm有没有分错，是跑简单二倍体流程吗，目前该真菌还没有染色体级别可供参考的基因组。

Can CRAQ be used as software for detecting haplotype assembly errors using hifi data?

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hello I have assembled two haplotypes using the hifiasm software based on HIC hifi ONT data. I am wondering if it is possible to utilize this software to inspect errors...

mycode :sbatch HiCPro_step1_hicpro1.sh error:sbatch: error: Invalid --time specification

Hello  thanks for your help

Hi, I'm currently assembling a fungal genome, which is approximately 40 (Mb) in size. I've encountered a peculiar phenomenon where the longest contig I have obtained is around 4 Mb...