JustinChu JupiterPlot issues

JustinChu / JupiterPlot

A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.

GNU General Public License v3.0

68 stars 11 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Synteny graph not representing alignment results: I appreciate your help

#48 BioJules closed 3 weeks ago
12
Labels

#47 aebaci opened 2 months ago
2
can this pipeline be added to a container?

#46 KristinaGagalova closed 3 months ago
4
CIRCOS ERROR cmd: circos -noparanoid -conf test.conf

#45 ykkim0127 closed 6 months ago
5
Problems with the aesthetics of the plot

#44 jacolmen closed 3 months ago
1
Effect of mapping parameters

#43 tanpham15 closed 3 months ago
2
Request: Option to always show all contigs

#42 alexweisberg closed 6 months ago
1
Can I retain some config files removed by your script?

#41 nzx9581 closed 6 months ago
2
Link files change chromosome names

#40 mpalmada closed 1 year ago
0
No Y chromosome

#39 imdanique closed 1 year ago
0
No links despite large regions of similarity visible in dot plot from MUMMER alignment

#38 mptrsen closed 12 months ago
13
Reciprocity of matching regions

#37 ckeeling closed 1 year ago
1
Set links between chromosomes

#36 Karimi-81 closed 6 months ago
2
Get chromosomal names/numbers on the "query", and alignment issue.

#35 siv-n closed 12 months ago
4
Running failure

#34 JQVazquez closed 3 years ago
2
Only a fraction of the represented scaffolds aligned to the reference.

#33 jprunier-ulaval closed 6 months ago
4
output genome coverage

#32 aafshinfard closed 2 years ago
0
output genome coverage

#31 aafshinfard closed 3 years ago
0
correct .PRECIOUS files

#30 aafshinfard closed 3 years ago
0
Fix problems on Mac OS

#29 JustinChu closed 6 months ago
1
max number of scaffs to plot

#28 aafshinfard closed 4 years ago
0
chromosome has no alignments!

#27 drashwinelkar closed 4 years ago
5
circos plotting error

#26 mjmillerlab closed 4 years ago
4
README.md: typo fixes

#25 jwcodee closed 4 years ago
0
Add option to render the scaffold IDs or equivalent

#24 JustinChu closed 1 year ago
1
Add option to change minimum MAPQ to be shown on plot

#23 JustinChu closed 4 years ago
1
Change path for Samtools

#22 wlaw13 closed 4 years ago
3
Reg: Some maintenance of the tool

#21 harish0201 closed 5 years ago
2
numbers of scaffold to render & their order

#20 scintilla9 closed 4 years ago
2
Change color of the output and replot

#19 scintilla9 closed 5 years ago
2
Change labels and re-plot

#18 gbdias closed 5 years ago
2
Add option to reorder reference and scaffolds iteratively

#17 JustinChu closed 6 months ago
1
Add option to remove chr names from output

#16 JustinChu closed 1 year ago
1
Add additional columns to seqOrder to show intended (median) location of alignment of scaffolds

#15 JustinChu closed 6 months ago
2
Add option to place overlapping contigs

#14 JustinChu closed 6 months ago
1
List of non-standard modules needed

#13 ckeeling closed 6 years ago
1
Experiment with minimap2 alignments

#12 JustinChu closed 5 years ago
0
Add option to easily change alpha of links

#11 JustinChu closed 1 year ago
1
Add option to allow for poor alignments to be used in visualization

#10 JustinChu closed 2 years ago
1
Add mode to intentionally drop out congruent links

#9 JustinChu closed 6 months ago
1
Create a demo with example assembly and reference file inputs

#8 JustinChu closed 2 years ago
0
Allow for scaffold names to be printed using an option

#7 JustinChu closed 6 years ago
1
Script error: Can't use an undefined value as an ARRAY reference

#6 JustinChu closed 7 years ago
2
recipe failure for the bed file

#5 mroach-awri closed 7 years ago
7
Show poorly aligned regions of the scaffold with some sort of mark (like how gaps are shown)

#4 JustinChu closed 6 months ago
1
Allow more global alignment solution to be used

#3 JustinChu closed 6 years ago
1
Show inversions relative to predominate orientation by twisting link

#2 JustinChu closed 6 years ago
1
Generate Make File-like workflow for generating intermediate files

#1 JustinChu closed 7 years ago
0