phasegenomics juicebox_scripts issues

phasegenomics / juicebox_scripts

A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats

GNU Affero General Public License v3.0

63 stars 10 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

agp2assembly not used for break contig

#34 socialhang opened 1 year ago
0
Convert .assembly file to .agp file

#33 tinyfallen opened 1 year ago
0
Cannot generate output files with juicebox_assembly_converter.py

#32 mixiaoluo88 opened 2 years ago
4
Using Juicer 1.11 output will not convert

#31 Hannah1746 closed 3 years ago
6
Fix off by one 2

#30 shawnpg closed 3 years ago
0
UnscaffoldedContigError: Contigs are not included in scaffolding output with when generating new SCAFFOLD after modifying in Juicebox 1.11.08

#29 tiramisutes closed 3 years ago
1
Fix off-by-one issues making FASTA and reports

#28 shawnpg closed 3 years ago
1
In response to issue, added more clarity about how to get .hic and .a…

#27 maximilianpress closed 4 years ago
0
agp2assembly.py produces a .assmbly file that shows scaffolds only in first chromosome

#26 gitcruz closed 4 years ago
7
whole contig debris + more

#25 maximilianpress closed 4 years ago
1
juicebox assembly converter for juicebox 1.11

#24 luciaalvarez95 closed 4 years ago
19
Swapped Length Discrepancy Error to Warning

#23 hhayleyj closed 5 years ago
0
Length discrepancy error

#22 hhayleyj closed 5 years ago
1
Assembly purger

#21 bnelsj closed 5 years ago
3
check fragment lengths

#20 maximilianpress closed 3 years ago
0
Handle non-sequential contig numbering in assembly converter script

#19 bnelsj closed 5 years ago
0
Add support for mixed fragment names

#18 shawnpg closed 5 years ago
0
Add simple chromosome name mode

#17 shawnpg closed 5 years ago
0
juicebox assembly converter no longer working

#16 aboyher closed 4 years ago
4
Allow converter script to recognize fragments

#15 shawnpg closed 5 years ago
0
conversion fixes

#14 maximilianpress closed 5 years ago
1
juicebox_assembly_converter.py off by one converting to agp

#13 erondeau closed 3 years ago
11
juicebox to chromosome bins fasta

#12 mictadlo closed 4 years ago
5
Why is -p false in run-assembly-visualizer.sh

#11 mictadlo closed 5 years ago
3
temp.scaffolds_FINAL.asm_mnd.txt does not exist or does not contain any reads.

#10 mictadlo closed 5 years ago
6
Create CODE_OF_CONDUCT.md

#9 shawnpg closed 5 years ago
1
Update issue templates

#8 shawnpg closed 5 years ago
2
Correct incorrect .assembly file test data, change scaffold naming

#7 shawnpg closed 5 years ago
0
Add Travis CI badge

#6 bnelsj closed 5 years ago
0
Add logo

#5 zeeev closed 5 years ago
0
adding logo to readme

#4 zeeev closed 5 years ago
0
Add scripts fix

#3 bnelsj closed 5 years ago
0
makeAgpFromFasta.py indentation

#2 rwhetten closed 6 years ago
1
add the initial scripts.

#1 maximilianpress closed 5 years ago
2