-
It would be interesting to implement the method Ane developed in Rabier et al. (2014). Ane has given permission and we need to make sure to give credit where due.
https://www.ncbi.nlm.nih.gov/pubme…
-
Dear Aouthr!
For now, allhic is the closest software for success to polyploidy in which I used.But I have a bewilderment.
When I use `Allele.ctg.table` pruning some hi-c signal, anchoring rate is ve…
-
Dear developers,
I encountered some issues while using Smudgeplot to predict polyploidy. The species I am studying is expected to be hexaploid based on flow cytometry analysis, but whether it is aut…
-
Hello!
Hope this message finds you well.
I want to extend my sincerest thank for developing PECAT, which has been an invaluable tool in my work.
Besides, I am very curious about the possibil…
-
Dear Author,
When performing genome survey via Illumina pair-end data, it showed that the genome size is 9, 700 or 1,400 Mb. However, when I assembled my Nanopore reads using Nextdenove with genome…
-
Hi there, I am working on a few hexaploid genome assemblies and wanted to try this tool for providing the inputs for EndHiC. I was wondering if this would be able to handle high ploidy levels? I have …
-
In #5 I asked about the `bulkSize` option in `runQTLseqAnalysis()` if:
>is it the case that this parameter should be the number of genome copies pooled, which for a diploid it would be 2x number o…
-
Hi @dfguan
Firstly, thanks for an interesting tool - it's proving to be really helpful.
Secondly, I wanted to get your opinion on the output of purge_dups with an (ancestrally) polyploid organ…
-
luiz's talk about how we develop/design/evolve sourmash: https://www.youtube.com/watch?v=0jpnP8NtRfc&feature=youtu.be
-
Based on a survey of the variant types used in CIViC as a starting point:
- SNVs (single nucleotide variants). e.g. `R175H`
- MNVs (e.g. dinucleotide variants). e.g. `VHL c.364_365GC>AT`
- Insert…