C-YONG

problem “Could not parse the header line”

1

 code：smoove genotype -d -x -p 20 --name 432-joint --outdir ./ --fasta ../../03_genome/genome1.3.fna --vcf merged.sites.vcf.gz ../. ./04_bam/432.sort.bam When i run the above code, i get this report, does it affetc...

We encountered the following error during the computation using the script. Could you help identify the possible cause? svs = lapply(list.files('pan_svs/', '.rds'), function(fn){ gr = readRDS(paste0('pan_svs/', fn)) gr$sample = gsub('(.)\.decomposed.svs.rds',...

Issue with cluster step in HapHiC – "Some fragments are missing / redundant" and fewer clusters than expected

18

Dear HapHiC developers, I am trying to use haphic cluster to perform clustering on my genome assembly. My organism has 20 chromosomes, and I used the following command: “~/soft/HapHiC/haphic cluster...

**1. What were you trying to do?** I want to perform variant detection on second-generation sequencing data based on the pan-genome constructed using Minigraph-Cactus **2. What did you want to...

samtools reheader error

6

Hello, software developer. I used VG to align a pangenome and generate the original BAM file, where the header sequence order is chr1, chr10, chr11. I wanted to replace the...

Question Regarding Low QV from Illumina Data Evaluation Compared to HiFi Data

4

Hi: I hope this message finds you well. I have recently assembled a haplotype-resolved T2T genome using HiFi, ONT, and Hi-C data. To evaluate the quality of my assembly, I...

Hello, I have constructed a graph-based pan-genome using MC, and then I used VG to align short-read data to the pan-genome. When I used abra2, the following error occurred. What...