-
**1. What were you trying to do?**
We want to find the snp and indels variation from the result vcf file BS_graph_call.vcf.
**2. What did you want to happen?**
We want to find the reason that w…
-
Here is a strange case of a missing gnomAD variant, 17-41228120-T-C. It appears in the gnomAD browser (https://gnomad.broadinstitute.org/variant/17-41228120-T-C?dataset=gnomad_r2_1_non_cancer), but n…
-
Hi Dengfeng,
I am using purge_dups to purge a plant genome generated with ~37x coverage of pacbio hifi reads. Cytological estimates for this species put the put the genome size 850Mb, and kmer anal…
-
Hi!
Can CHOP be used to do the actual read mapping, or does it just create a fasta file that I e.g will need to index with BWA and then map reads to? If so, I assume my final alignments will be rel…
-
Hi,
I have been trying to incorporate Eggnog Mapper into a genome annotation pipeline ; and find that when using the "Metazoan" reference database on an annotation of a fish genome, I sometimes get…
-
At 70 genomes and 109GB of graph data
```
-rwxr----- 1 kevin kevin 109G Jun 26 08:10 pangenome.lemongraph
-rwxr----- 1 kevin kevin 8.0K Jun 26 08:42 pangenome.lemongraph-lock
```
Not sure why, …
-
Hello,
I'm currently analyzing a substantial dataset comprising 11,743 genomes of different _Enterococcus_ species, including over 20 outgroup genomes from the same family and order. because of the…
-
**1. What were you trying to do?**
Mapping Illumina WGS data to a cactus-minigraph pangenome.
In case it is relevant, the pangenome was constructed with 5 marsupial genomes, which have a few lon…
-
We have previously discussed adding metagenomics compatibility by running fly in meta mode and doing genome binning.
-
Hi,
I apologize in advance for the lack of code examples but I have to estimate computational resources before starting the project and I was hoping to get some guidance.
We are working on a complex…