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Hello, I am running this pipeline on a hifiasm (v0.19.5) assembly and encountered an error in the rule count_haplotype_markers. Below is the error message:
```
Creating a new cluster: (C1.7)40…
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Some DHPS/DHFR joint phenotypes confer S-P/IPTp resistance. Ability to analyse phenotypes across genes jointly would be valuable here, though if there is just this one usecase, it may be easier to jus…
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A clear procedure needs to be developed to gather inputs to run each new assembly:
- Two assembled haplotypes (same contig names);
- Optional NCBI gene/rna/protein taxon id and downloaded fasta fil…
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Hello, arangrhie,
Merqury has proven to be an excellent tool for evaluating genomes.
I currently possess a haplotype-resolved genome from an autotetraploid species, which includes four haplotype…
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**1. What were you trying to do?**
I used `vg rna` to build a spliced pangenome and a pantranscriptome with a GFA file from PGGB and a gff3 file. Similarly, I used `vg autoindex` to build index f…
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Hi there, could I use Clair3-RNA to haplotype resolve my RNA-Seq reads at the isoform level? i.e. could I map my reads to a transcriptome instead of a genome and obtain haplotype resolution.
Thanks…
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Hi,
What do you think about the possibility to view the mapped assembly as tracks in IGV? That could be shown (next to the reads), if files are included in the scout config?
Currently Nallo out…
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Hello,
Thank you for making this program.
I am hoping to resolve some haplotype switch errors in my regions of interest, and I think Methphaser would be very nice to try out.
My regions of int…
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Hi jannatjiaz,
I am so interested in your ChromoDethripsis methods. I am curious about one issue:
python CTResolveLowDensity.py
--chromosome
--bam
--readnames
--haplotype1_reads
--hapl…
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Hello!
I was just wondering if this software would be useful to determine full haplotypes or quasispecies in "multiple" CRISPR edited polyclonal mixtures (for example 2 sgRNA's cutting close to each …