Comments (7)
Can you show me the whole log and the plots produced by subphaser? I suspect that the genome is not well phased.
from subphaser.
from subphaser.
from subphaser.
from subphaser.
from subphaser.
As clearly shown by the results, the subgenomes are not well assigned, because there are too few differential kmers between subgenomes. It may be artifactual or natural. My suggestions (refer to the Supplementary Material):
- Check the HiC contact map whether there are too many switch errors between subgenomes. If not, it is natural.
- If natural, it may be because 1) there are too many recombinations between subgenomes after hybridization, or 2) their progenitors are too close (possible autopolyploid) to distinguish. In these cases, subgenome phasing is meaningless and subphaser will not work.
So many chromosomes may also be an issue. You can have a try to reduce the number of homeologous chromosome sets by setting the config like:
1 2 3
...
13 14 15
16
17
18
...
75
76
77
Remove check point files by rm tmp/*ok
before re-runing to avoid confusing.
from subphaser.
Thank you for your quick reply. I will take a try
from subphaser.
Related Issues (20)
- Changing mutation rate HOT 1
- Invalid specifier: '>=3.6:' HOT 1
- Only one pair of homologous chromosomes were not phased HOT 5
- matplotlib raise RuntimeError ('Invalid DISPLAY variable') HOT 2
- Unbalanced of chromosomes number and differential kmers number among subgenomes HOT 1
- `TEsorter` cannot find `rexdb` in Singularity container HOT 3
- Singularity container fails if environmental variable `R_LIBS_USER` is set HOT 2
- No differential kmers HOT 2
- ValueError: All singletons are not allowed HOT 1
- ValueError: 0 kmer with fold > 2. Please reset the filter options. HOT 1
- cannot allocate memory HOT 13
- 亚基因组分析 HOT 2
- Getting location of subgenome specific TEs HOT 2
- Suggestion for specific settings to improve subphasing HOT 6
- kmer 13 or less gives a lot of broken pipe errors HOT 5
- 两套单倍型分配不平均 HOT 2
- OSError: [Errno 12] Cannot allocate memory HOT 2
- OSError: /usr/lib/libdrmaa.so.1.0: cannot open shared object file: No such file or directory HOT 1
- FileNotFoundError: [Errno 2] No such file or directory: 'sg.config''
- OSError: [Errno 12] Cannot allocate memory HOT 8
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from subphaser.