issues
search
AmpliconSuite
/
AmpliconSuite-pipeline
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
Other
58
stars
28
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Analysis of long-read sequencing data
#68
stephchid
opened
1 month ago
1
mosek.Error: (1001) The license has expired.
#67
jingydz
opened
2 months ago
7
How to Differentiate Amplification on eccDNA vs. Linear Genome?
#66
talhamufeed
opened
3 months ago
1
No eccDNA detection yet
#65
talhamufeed
closed
3 months ago
6
What happens if you use a smaller Seed?
#64
newpest
opened
3 months ago
3
Tumor-only vs Normal-paired
#63
yaosichao0915
closed
1 month ago
5
GroupedAnalysis mode failure when more than 1 normal sample provided
#62
auberginekenobi
closed
1 month ago
5
Guidance on creating reference genome files for a new species
#61
YxZhang-XHCY
opened
5 months ago
2
Pipeline stalling at plotting SV view
#60
at10101
closed
5 months ago
4
An error with MOSEK call in AmpliconArchitect.py
#59
carrie1s
opened
6 months ago
8
stuck in SV plotting even set--runmode as `- CYCLES`
#58
Serene0503
opened
6 months ago
6
Shared project email notification not sending on prod
#57
jluebeck
closed
7 months ago
0
How to understand different results of AmpliconArchitect in different servers?
#56
JFanbio
opened
7 months ago
5
how the pipeline generate CNV_CALLS_pre_filtered.bed file?
#55
JFanbio
closed
6 months ago
8
There are some small bugs in singularity running scripts
#54
panxiaoguang
closed
5 months ago
2
interchange between species A and B in data repo
#53
Shuixin-Li
closed
8 months ago
2
AttributeError: module 'pomegranate' has no attribute 'NormalDistribution'
#52
Tina04021997
closed
9 months ago
2
run Ampliconsuite-pipeline on WGBS data
#51
QLZhouBio
opened
10 months ago
8
Amplicon Classifier error in grouped analysis mode using mamba installed pipeline
#50
bweasels
closed
10 months ago
5
Unstable dev
#49
jluebeck
closed
11 months ago
0
Update GUIDE.md
#48
jluebeck
closed
11 months ago
0
cycle view
#47
eesiribloom
opened
1 year ago
1
Update install.sh
#46
auberginekenobi
closed
1 year ago
3
Support for non-human species
#45
Chao-Guo-hub
closed
1 year ago
4
Handling BAMs aligned with BWA-MEM -m flag
#44
tjbencomo
closed
1 year ago
2
Request for benchmarking dataset
#43
aarthi-mohan
closed
12 months ago
4
cnv_prefilter
#42
uretaj
opened
1 year ago
2
Version mismatch between Git Clone and Docker.
#41
iamyingzhou
closed
1 year ago
9
Directory issue
#40
uretaj
closed
1 year ago
6
Suggestions for arguments to AA to tweak?
#39
tischfis
opened
1 year ago
1
add samtools_path
#38
solo7773
closed
1 year ago
0
Add custom samtools
#37
solo7773
closed
1 year ago
1
Missing seed_trimmer.py in the scripts directory
#36
solo7773
closed
1 year ago
2
Long run time with *_CNV_CALLS_pre_filtered.bed
#35
WeijiaSu
opened
1 year ago
4
ValueError: cannot convert float NaN to integer
#34
WeijiaSu
closed
1 year ago
12
b37 reference genome
#33
yliu34
closed
1 year ago
5
CNVKit encountered a non-zero exit status. Exiting...
#32
jingydz
closed
1 year ago
7
please update ampliconarchitect docker image
#31
ryao-mdanderson
closed
1 year ago
12
In most runs AA_CNV_SEEDS.bed files are empty
#30
Yumo-Xie
opened
1 year ago
7
IndexError: list index out of range
#29
Cathy94
closed
1 year ago
9
changes to merge GPN container with Jens' container
#28
edwin5588
closed
2 years ago
0
AA error in insert_sdevs
#27
Tina04021997
closed
2 years ago
4
some suggestions
#26
panxiaoguang
opened
2 years ago
2
Docker permissions
#25
MrDotOne
opened
2 years ago
18
empty AA_CNV_SEEDS.bed file
#24
gneedle1
closed
1 year ago
4
less number break points
#23
sarmadmehmood89
closed
2 years ago
2
Bump numpy from 1.16.6 to 1.21.0 in /docker/requirements
#22
dependabot[bot]
closed
2 years ago
0
reference genome path
#21
gneedle1
closed
1 year ago
1
Dependency regex no longer supports python 2
#20
auberginekenobi
closed
2 years ago
1
mm10 files in data_repo are missing
#19
danielagerovska
closed
2 years ago
7
Next