PacificBiosciences/pb-CpG-tools

Issues

• modification probability vs discretized modification probability

  #69 opened 5 months ago by Jinyulin515
  1

• The ML threshold for a reliably methylated cytosine

  #70 opened 5 months ago by leon945945
  1

• modsites-mode

  #68 opened 5 months ago by wittney-m
  3

• Read sequence is too short for MM tag offsets in bam record

  #60 opened 8 months ago by hasindu2008
  2

• Without the MM and ML auxiliary tags

  #61 opened 8 months ago by lixiang117423
  0

• Tools for mapping methylation and expression relationships

  #62 opened 8 months ago by Wenwen012345
  5

• cannot get 5mc probability Revio platform

  #65 opened 8 months ago by Duyh814
  4

• # Questions about jasmine

  #66 opened 8 months ago by xiangpingyu
  1

• Criterion for error: Read sequence is too short for MM tag offsets in bam record

  #67 opened 8 months ago by aewrwdw
  1

• About haplotype output

  #64 opened a year ago by woshiakai5525
  3

• Empty BED file

  #63 opened a year ago by roybarkan2020
  0

• Add to bioconda

  #59 opened a year ago by mobilegenome
  1

• need clarifications on the workflow

  #58 opened a year ago by splaisan
  1

• the question about hap1 and hap2

  #57 opened a year ago by crazysummerW
  2

• Error: Read sequence is too short for MM tag in record: {qname}

  #56 opened a year ago by glogsdon1
  7

• difference betwwen -m denovo and reference

  #54 opened a year ago by Duyh814
  3

• Run the pipeline on prokaryotic dataset

  #49 opened a year ago by pailloufat-stack
  7

• Suggestions for indicating methylation regions on circos plots?

  #53 opened a year ago by Wenwen012345
  1

• genetic variants on CpG sites

  #55 opened a year ago by qsonehara
  3

• A pipeline for known parental haplotypes?

  #52 opened a year ago by gokalpyildirir
  4

• Primrose unavailable

  #51 opened a year ago by scorreard
  2

• Can I use CpG tools if I have other basemods in the file

  #48 opened a year ago by mrvollger
  2

• Availability of jasmine

  #50 opened a year ago by PengNi
  1

• Error with haplotagged BAM files - Unexpected HP tag format

  #47 opened a year ago by Audald
  4

• Is CpG status predicted at insertion variants?

  #40 opened 2 years ago by elcortegano
  4

• Supplementary reads not processed - aligned_bam_to_cpg_scores

  #46 opened a year ago by Audald
  4

• Segmentation fault with CRAM files - aligned_bam_to_cpg_scores

  #45 opened a year ago by Audald
  3

• avg mod score and avg unmod scores

  #44 opened a year ago by olaraym
  4

• how to prepare input data for phasing 5mc methylation analysis?

  #43 opened 2 years ago by oceancongliu
  6

• running error

  #42 opened 2 years ago by yueqitaoo
  5

• aligned_bam_to_cpg_scores v2.1.0 raises an error

  #41 opened 2 years ago by JBinkowski
  4

• strand specific extraction

  #37 opened 2 years ago by xiaoyunguo
  2

• ModuleNotFoundError: No module named 'packaging'

  #35 opened 2 years ago by krobison13
  2

• error installing pb-CpG-tools

  #34 opened 2 years ago by Mjaraespejo
  2

• DtypeWarning: Columns (8) have mixed types

  #33 opened 2 years ago by elcortegano
  2

• Error - pileup_model model

  #26 opened 2 years ago by jainy
  13

• Models suitable for plants?

  #36 opened 2 years ago by hrpelg
  2

• Runtime dependency conflict

  #38 opened 2 years ago by williamrowell
  0

• question for output

  #22 opened 2 years ago by hmyh1202
  5

• Error: concurrent.futures.process.BrokenProcessPool

  #31 opened 2 years ago by yimingzhu100
  3

• Program stalled/zombified

  #15 opened 2 years ago by oushujun
  7

• Include phaseset information

  #28 opened 2 years ago by AngelaQChen
  1

• Why skip 40 aligned_pairs?

  #29 opened 2 years ago by bing2022ca
  1

• What is the different between pb model and HK model

  #30 opened 2 years ago by hmyh1202
  1

• Can I used minimap2 for alignment ?

  #27 opened 2 years ago by hmyh1202
  1

• cg_sites_dict UnboundLocalError

  #20 opened 2 years ago by sunkelb
  3

• How to Select pileup_mode ?

  #18 opened 2 years ago by hmyh1202
  1

• modification probability

  #17 opened 2 years ago by yuntwang
  1

• Need deduplication for aligned BAM ?

  #19 opened 2 years ago by hmyh1202
  1

• Transfer MM and ML tags from one BAM file to another?

  #16 opened 2 years ago by elcortegano
  2