Yibin Wang

Hi， Error of `ERROR Cannot open bamfile sample.clean.bam (gzip: invalid header)` occurred. How did you generate the `sample.clean.bam` file? And what is the version of samtools your used? Please provide...

Hi, You should run command with nohup by this way: ```bash nohup samtools view -bt genome.polish.fasta.fai sample.clean.sam -o sample.clean.bam & ``` It is an error to output the result to...

Hi, I think this error message may be caused by the samtools version being too old, recommend using v1.9.0. Or you can try using this command to convert sam to...

Are you sure completed `bwa sampe`, `truncated file` may indicate the incorrect sam file. You should check your sam file.

Hi, I have tested replacing the first two columns with NA, and it worked. Please provide some of your allele table.

Hi, > Can I provide two restriction sites in the -e option ? You can use `-e Arima` in the latest version of ALLHiC_partition. ``` $ ALLHiC_partition Usage: ALLHiC_partition -r...

You can try setting 47 groups or more. From our experience, the final grouping of chromosomes can be determined using Hi-C heatmaps. Too small groups can be discarded manually. Or,...

Hi, The final result of `ALLHiC_prune` is `prunning.bam`. You can use the development version of `ALLHiC_prune` (https://github.com/sc-zhang/ALLHiC_components/tree/main/Prune` ). This version does not generate intermediate files and has a speed increase.

Hi, ALLHiC_corrector is developed for chimeric contig correction which will lead to misassembly for ALLHiC. I think simple diploid genome assembly from hifiasm could skip ALLHiC_corrector. Then, you can import...

Hi~ Have you tried recompiling the package? This error can be resolved by recompiling. ``` cd Prune export CPPFLAGS="-I/path/to/htslib/include" export LDFLAGS="-L/path/to/htslib/lib" make ```