AmpliconSuite/AmpliconSuite-pipeline

Issues

• How do i create a `mm10_viral` reference?

  #69 opened a month ago by kopardev
  1

• Tumor-only vs Normal-paired

  #63 opened 3 months ago by yaosichao0915
  5

• GroupedAnalysis mode failure when more than 1 normal sample provided

  #62 opened 3 months ago by auberginekenobi
  5

• Analysis of long-read sequencing data

  #68 opened 3 months ago by stephchid
  1

• mosek.Error: (1001) The license has expired.

  #67 opened 4 months ago by jingydz
  7

• How to Differentiate Amplification on eccDNA vs. Linear Genome?

  #66 opened 4 months ago by talhamufeed
  1

• No eccDNA detection yet

  #65 opened 4 months ago by talhamufeed
  6

• What happens if you use a smaller Seed?

  #64 opened 5 months ago by newpest
  3

• please update ampliconarchitect docker image

  #31 opened 2 years ago by ryao-mdanderson
  12

• Guidance on creating reference genome files for a new species

  #61 opened 7 months ago by YxZhang-XHCY
  2

• An error with MOSEK call in AmpliconArchitect.py

  #59 opened 8 months ago by carrie1s
  8

• Pipeline stalling at plotting SV view

  #60 opened 7 months ago by at10101
  4

• how the pipeline generate CNV_CALLS_pre_filtered.bed file?

  #55 opened 8 months ago by JFanbio
  8

• stuck in SV plotting even set--runmode as `- CYCLES`

  #58 opened 8 months ago by Serene0503
  6

• How to understand different results of AmpliconArchitect in different servers?

  #56 opened 8 months ago by JFanbio
  5

• Shared project email notification not sending on prod

  #57 opened 8 months ago by jluebeck
  0

• interchange between species A and B in data repo

  #53 opened 10 months ago by Shuixin-Li
  2

• run Ampliconsuite-pipeline on WGBS data

  #51 opened a year ago by QLZhouBio
  8

• AttributeError: module 'pomegranate' has no attribute 'NormalDistribution'

  #52 opened a year ago by Tina04021997
  2

• Amplicon Classifier error in grouped analysis mode using mamba installed pipeline

  #50 opened a year ago by bweasels
  5

• Request for benchmarking dataset

  #43 opened a year ago by aarthi-mohan
  4

• cycle view

  #47 opened a year ago by eesiribloom
  1

• Support for non-human species

  #45 opened a year ago by Chao-Guo-hub
  4

• Handling BAMs aligned with BWA-MEM -m flag

  #44 opened a year ago by tjbencomo
  2

• cnv_prefilter

  #42 opened a year ago by uretaj
  2

• Docker permissions

  #25 opened 2 years ago by MrDotOne
  18

• Long run time with *_CNV_CALLS_pre_filtered.bed

  #35 opened 2 years ago by WeijiaSu
  4

• Suggestions for arguments to AA to tweak?

  #39 opened 2 years ago by tischfis
  1

• In most runs AA_CNV_SEEDS.bed files are empty

  #30 opened 2 years ago by Yumo-Xie
  7

• Directory issue

  #40 opened a year ago by uretaj
  6

• Version mismatch between Git Clone and Docker.

  #41 opened 2 years ago by iamyingzhou
  9

• reference genome path

  #21 opened 2 years ago by gneedle1
  1

• Missing seed_trimmer.py in the scripts directory

  #36 opened 2 years ago by solo7773
  2

• ValueError: cannot convert float NaN to integer

  #34 opened 2 years ago by WeijiaSu
  12

• empty AA_CNV_SEEDS.bed file

  #24 opened 2 years ago by gneedle1
  4

• b37 reference genome

  #33 opened 2 years ago by yliu34
  5

• CNVKit encountered a non-zero exit status. Exiting...

  #32 opened 2 years ago by jingydz
  7

• IndexError: list index out of range

  #29 opened 2 years ago by Cathy94
  9

• Always stuck at "Plotting SV View"

  #17 opened 3 years ago by notchw
  6

• AA error in insert_sdevs

  #27 opened 2 years ago by Tina04021997
  4

• some suggestions

  #26 opened 2 years ago by panxiaoguang
  2

• less number break points

  #23 opened 2 years ago by sarmadmehmood89
  2

• mm10 files in data_repo are missing

  #19 opened 3 years ago by danielagerovska
  7

• broken scripts

  #18 opened 3 years ago by davidhoover
  1

• Dependency regex no longer supports python 2

  #20 opened 3 years ago by auberginekenobi
  1

• TypeError: 'NoneType' object is not callable

  #16 opened 3 years ago by zhangheng43
  16

• Parameter for cnvkit in Readme need change

  #14 opened 4 years ago by Si-Nan
  1

• run_paa_script.sh in Docker has permission problem to write

  #13 opened 4 years ago by Si-Nan
  1

• [AmpliconArchitect] MD tag not present

  #12 opened 4 years ago by zhang919
  8

• some question about PrepareAA

  #11 opened 4 years ago by zhang919
  8