Comments (6)
As you have got a well split of 4 subgenomes, you can finally input the assignments of 4 subgenomes via -sg_assigned
. This option will use the assignments directly, but not re-assign subgenomes. The input is in the format of the previous output *.chrom-subgenome.tsv
, like:
#chrom subgenome
3_R4 R4
...
7_R5 R5
...
2_s3 s3
...
3_s1 s1/2
...
from subphaser.
Thanks a lot! It just worked perfect! Is there a way I can specify the color to each subgenome?
You should receive a nobel for that tool. So awesome!
from subphaser.
just found the right commands, please ignore the message above, but the nobel thing still holds true :-)
from subphaser.
After using the hex color parameters and assigned subgenome options the circos plot changed a lot. Any way to fix or improve this? In particular the purple SG is not evident after using the hex and sg_assigned parameters
with command: subphaser -i $REF -c config_chr.txt -pre ref -p 20 -cleanup
with command: subphaser -i $REF -c config_chr.txt -pre 4sg_hex -p 20 -cleanup -sg_assigned assigned.txt -colors "#f37d38,#f9a64a,#452f91,#9097cb"
from subphaser.
It should be because S1/S2 have no speciefic kmers, and for s3, speciefic kmers distributed unevenly. At present, there may be no simple options to work well. You may try again to input one combination of two or three subgenomes every time, and check whether the results are reiable.
from subphaser.
Thanks, indeed removing S2 chromosomes improve a lot. In fact, S2 chromosomes are only homologs of S1 and not truly another different subgenome...
from subphaser.
Related Issues (20)
- Error in os.link(figfile, dstfig) HOT 3
- IndexError: cannot do a non-empty take from an empty axes. HOT 10
- Failed to install SubPhaser HOT 9
- ModuleNotFoundError: No module named 'TEsorter' HOT 4
- The output subgenomes are not paired HOT 4
- 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
- kmer 13 or less gives a lot of broken pipe errors HOT 5
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.