virajbdeshpande/AmpliconArchitect
AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
PythonNOASSERTION
Issues
- 2
how to find breakpoint count in AA result?
#146 opened by aw2222222222 - 0
Cycle view
#145 opened by newpest - 2
Chromosome Coordinate on the amplicon cycles is 1 bp less than the real genome coordinate
#144 opened by JungnamChoLab - 14
- 5
- 8
AmpliconArchitect - Licensing & Bioconda
#120 opened by DSchreyer - 3
coverage.stats
#141 opened by pawanchk - 6
question of use AA for other species ref
#140 opened by fanch1122 - 6
MOSEK: Failed to solve to optimality
#139 opened by shwong-tw - 3
- 5
ZeroDivisionError: float division by zero
#138 opened by ZHONGHONGXIN - 1
mosek commercial license
#137 opened by phansol - 1
Release tags missing
#136 opened by jbedo - 1
AA amplicon number:NA
#131 opened by jingydz - 2
Always stuck at "Optimizing graph copy number flow"
#127 opened by szbssg - 3
output files
#132 opened by jennyp76 - 1
# of discordant reads
#133 opened by hj6-sanger - 1
SVs calls among output files
#130 opened by l0ka - 1
CNV need to consider sample purity and ploidy?
#128 opened by Bio-LiHe - 1
Reproducibility of AmpliconArchitect
#126 opened by EunchongHuang - 4
- 2
- 5
Results owned by root
#123 opened by MrDotOne - 1
RNA-seq data as the input for AA
#122 opened by EunchongHuang - 3
- 4
running time and usage of AmpliconArchitect
#118 opened by lwlive - 2
ValueError: cannot convert float NaN to integer
#117 opened by acticu - 2
Empty cycles, graph , and SV view files
#115 opened by Tina04021997 - 0
- 1
WGBS/ATAC data as input for AA
#114 opened by juheon - 5
- 5
BAM files from Isaac aligner
#113 opened by AndrewC160 - 1
Upgrading to Mosek v9
#103 opened by erling-d-andersen - 7
detect ecDNAs from circle-seq data
#99 opened by lanliting - 1
Can't get AA_DATA_REPO file
#112 opened by enshiba - 1
cannot find coverage.stats in data repo
#110 opened by najoshi - 0
AttributeError
#111 opened by gbnci - 2
How to get AA data repo?
#109 opened by najoshi - 5
[root:WARNING] dnlists do not match 756 752
#108 opened by shaka-emperor - 12
Downsampling only on AA step or PrepareAA step
#105 opened by ysbioinfo - 1
- 2
Always stuck at "Plotting SV View"
#104 opened by notchw - 2
Long read sequencing + AA to call ecDNA?
#102 opened by alhafidzhamdan - 1
Unable to run after pulling latest image
#101 opened by lindakohn - 2
Would pre-filtered bam file accelerate the runtime
#100 opened by shwong-tw - 2
IOError
#98 opened by panxiaoguang - 2
coverage.stats file doesn`t exist
#97 opened by lanliting - 4
coverage.stats is not generated?
#96 opened by vodkatad - 3
Issues in installing AA
#95 opened by lanliting - 0