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When extracting a subgraph using a BED file via `-b` the resulting subgraph contains all BED range(s) specified plus all nodes between these ranges which are not touched by any path!
It would be nic…
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Hi,
I was wondering if the RAW data used to train the ONT model on R10.4.1 chemistry is publicly available. The ones on the GIAB FTP server are all R9.4.1. If so, could you point me to where these fi…
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**1. What were you trying to do?**
I would like to convert haplotype sampled GBZ graph to GFA, with GRCh38 path written as rGFA tags.
**2. What did you want to happen?**
Generate an GFA f…
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I ran through the example of creating a graph of two E. coli genomes on the [wiki](https://github.com/vgteam/vg/wiki/VG-RDF,-the-Ensembl-bacteria-E.-coli-genome-hack-attack) and everything has worked …
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Generate a toy chain file between GRCh38 T2T-CHM13v2.0:
```
$ echo -e "chain 2089 chr1 248956422 + 123985788 123986987 chr1 248387328 + 123418353 123419553 2482\n340 700 701\n159" > input.chain
$ …
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## Short description of the problem
Greetings everyone, Meren asked to use this channel to discuss this topic from the discord server "https://discord.com/channels/1002537821212512296/1263173335479…
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Hi,
I want to use your HGSVC graph for my own analysis. In your ftp website, I saw many different graphs. As following:
1) https://cgl.gi.ucsc.edu/data/giraffe/mapping/graphs/for-NA19240/hgsv…
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This is not really a software issue, but a general question about the paraphrase algorithm. If it is aligning reads to one member of the gene family, how can it distinguish if a read is from a gene or…
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Hi there,
Thanks for developing this tool!
I was trying to run minimap2-aligned BAM files with Sawfish and encountered an error saying 'no rq tag'. I checked PacBio's doc and found it is the tag…
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### 1. Lesson Topic
Pangenomics analysis in prokaryotes and Topological Data Analysis
### 2. Lesson Language
English
### 3. Draft materials
https://czirion.github.io/pangenomics-workshop/
### 4.…