-
### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
What are the collection types and names? Example:
- Glycine/max/annotations/Lee.gnm3.ann1.ZYY3
…
-
Do vg filter out some variants during the construction of the pan-genome, and if so, what are the criteria for filtering? The number of variations in the pan-genome is reduced compared to the variatio…
-
When ran "query_pan_genome -a difference" it came up with
MacBook-Pro:test kenken$ query_pan_genome -a difference -o difference --input_set_one CAS988.gff,D14_15_08Ph.gff --input_set_two E09_10_13P…
-
Hello! I get the result of pangenome. but I don't know the meaning of the file. like pan-genome.wga.conensus.stats,pan-genome.wga.core.stats, pan-genome.wga.newseq.stats and files in tmp. like An-1.co…
-
Dear all,
I have been having the following issue when installing panX. I followed the steps as in the site and used miniconda as indicated.
`Traceback (most recent call last):
File "./panX.py…
-
Hello,
I was curious to know how annotation is handled after 2 dbg graphs are merged using VariMerge? Is there an annotation tool (for bacteria) that the authors of this software would recommend al…
-
$query_pan_genome -a difference --input_set_one 1.gff,2.gff --input_set_two 3.gff,4.gff,5.gff
Error: Cant access the groups file: clustered_proteins
Usage: query_pan_genome [options] *.gff
Perfor…
-
(panX) anna@Anna-PC:~/work/pan-genome-analysis$ sudo sh run-TestSet.sh
Traceback (most recent call last):
File "./panX.py", line 6, in
from pangenome_computation import pangenome
File "/h…
-
### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
What are the collection types and names? Example:
- Arachis/stenosperma/annotations/V10309.gnm1…
-
Hello
I am teaching myself how to run panX using TestSet. Here is the command I run exactly following the instructions.
./panX.py -fn data/TestSet/ -sl TestSet -t 32 > TestSet.log 2> TestSet.err
…