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Hi,
I was wondering if I would like to calculate coverage across the genome for specific window size (ex. 100kb) using a BAM file, do I need to supply a reference genome file when I run PathDepth? Or…
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how is the alignment between two genes represented
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Dear Devon,
Thank you so much for developing this great tool! My colleague recommended bwa-meth and MethylDackel to me.
Recently we developed a haplotype-resolved diploid human genome, where one…
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Hi,
We are looking to optimize the polishing step for reconstructing a plant genome using PacBio HiFi reads (Q30). Specifically, we tested both NextPolish and NextPolish2, followed by a variant cal…
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Hi,
Is VACmap set up to do genome vs genome alignments? I could run in -mode L, however an assembled genome would have much fewer errors.
thanks.
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Hi @imk1,
Although I know that the main purpose of HLPER is not to transfer protein-coding genes, I wonder if Halpes has been tested for this task.
Let me explain my problem: I have two non-model …
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**Describe the bug**
`Illegal instruction (core dumped)` errors when trying to view any alignments with the same args (`$ gw -b input.bam refs.fasta -r "$ACCESSION"`) as used with gw v1.0.0.
**T…
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I've been trying to use this program to run an MK test using VCF files from the 1000 genomes project. However, I'm getting some really strange results with this method, and I'm worried I may be doing …
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Hello, I have a problem with the last parameter selection now, my purpose is to use the obtained maf file to draw circos collinearity alignment diagram, but the drawn graph has not been very good, and…
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Hello, When I used the GCI software to assemble my T2T genome, the following error occurred. What happened?
Used arguments:{'reference': '/export/home/zzl/YQ/Genome/Mel.genome.fa', 'hifi': ['/exp…