-
Hi All,
I am using pseudofinder to find pseudogenes in Vibrio cholerae isolates. I am using the blast nr database, but the blast stage is taking long on just one sample (over 24 hours and still run…
-
Hello SUPPA crew!
I've been having some issues with getting the IDs to match up between the abundance file and my ioe file. Here's what I'm working with...
GCF_000337935.1_Cliv_1.0_genomic.gt…
-
Incorporate the 57 gene ACMG blacklist
-
https://github.com/fmalmeida/bacannot/blob/7fb675b1688d3d2af85f7cf206ce0fc6a1e82858/modules/MGEs/islandpath.nf#L22
Line 22 of `islandpath.nf` detect if there is CDS in gbk file. However, when annot…
-
Hi,
I'm trying to use the sleuth function by providing a reference genome (does the reference genome also have to be annotated by prokka with the recommended flags?) with the annotate function.
B…
-
First hints for ideas:
- https://github.com/nigyta/dfast_core
- https://github.com/filip-husnik/pseudofinder#how-does-pseudofinder-detect-pseudogene-candidates
-
Hello @ValWood
Because I will use the genome sequence for the allele qc, I did some sanity checks. Below is what I have found. I guess the pseudogenes are expected, but why keep CDS that have stop…
-
Hello,
**Describe the bug**
I have a demultiplexed (bcl2fastq) single cell dataset, which i want to map and count. The design is as follow :
```
R1: Read 1 (26 nt) including the cell specific b…
-
Hi there,
I recently applied pseudofinder to a large set of genomes and I applied a filter to remove certain pseudogenes close to the edges of contigs. I think this makes sense for pseudogenes clas…
-
Many of the supported class II alleles are combinations of A and B alleles. Example:
```
DQA1*01:01-DQB1*02:01
```
Typical HLA typing protocols only return a list of individual alleles, not th…