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Hi Dinh,
I'm running your tool to extract methylation haplotypes from bam files, and I'm currently comparing the reads displayed in IGV with the methylation haplotypes generated from your tool. I'm…
caalo updated
6 years ago
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In the following data: [data.tar.gz](https://github.com/user-attachments/files/16457383/data.tar.gz)
there is exactly one single-end short read in `input.fasta` and two sets of haplotypes, `full.fa.g…
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**The bug**
I'm experiencing inconsistent (worse) results when generating text in multiple separate calls versus a single continuous generation. Specifically, using repeated calls to `gen` or `sele…
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Hi Im running the tool on 1 haplotype with a reference mode, using 240 GB and 32 Cores. I got this error.
[M::main] CMD: minimap2 -a -I 10G --eqx -x asm5 -t 4 --secondary=no /cbio/projects/031/moha…
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Hello,
I have encountered a weird issue when using minimap2 to do whole genome alignment. My data conatins a short assembly A (haplotype) and a long assembly B (diploid). When I used the assembly A a…
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Hello! I am running into an issue with `emase-zero` as implemented in `kbchoi/emase:latest`, getting the error:
`ERROR LOADING TRANSCRIPT LENGTH FILE ; UNKNOWN HAPLOTYPE NAME: PAR`
The issue is th…
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Hello Mr.Ruan,
I'm new to bioinformatics and genome assembly. I noticed SNV-Cov plot might be used for the redundancy in diploid genome. But, if I map the hifi reads of the child to the haplotype ass…
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See last cell of the [Haploytpe notebook](https://github.com/ga4gh/vrs-python/blob/main/notebooks/Haplotypes.ipynb). Enref on a haplotype should encode all nested ga4gh-identifiable objects by their `…
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Dear all,
I'm here for the first time in the community and have been trying for some time to obtain a pangenome to use as a reference for mapping short reads using `vg giraffe` and subsequent varia…
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Input: PacBio long read, HiC and Illumina short read data
Assembly: Canu v2.1.1 and then run my assembly through purgeHaplotigs
Variants: FreeBayes
I process HiC and PacBio files as recommended …