FelixKrueger/Bismark

Issues

• bismark(err): bowtie2-align died with signal 13 (pipe)

  #712 opened a month ago by wydsqgg524
  1

• Speed up merge_individual_BAM_files

  #707 opened 2 months ago by MilosCRF
  4

• Better Handling of Bismark2Report Uninitialized Error due to missing nucleotide key in nucleotide.stats report

  #711 opened a month ago by rhondene
  0

• Question about Bismark's Handling of Mismatches and Deletions

  #710 opened 2 months ago by hmu-youbai
  1

• question about mapping efficiency

  #709 opened 2 months ago by Marh32
  7

• Bismark silently outputs incorrect results when UMIs are added using Illuminas bcl-convert

  #699 opened 3 months ago by lars-work-sund
  7

• Issue with Alignment Results Using Soft-Masked Genome in Bismark

  #705 opened 2 months ago by Chanspace
  3

• Visualizing the CpG, CHG and CHH in Seqmonk

  #704 opened 2 months ago by lahyusof
  1

• Forward read data look great, paired end and reverse reads look erroneous

  #708 opened 2 months ago by robertocnava
  2

• SNAKEMAKE wrapper: How to add multicore?

  #706 opened 2 months ago by kenji-yt
  1

• Help with interpretation of M-bias plot

  #701 opened 2 months ago by xinyun-stacy-li
  2

• Query about including C in unknown context when calculating methylation proportions

  #703 opened 2 months ago by lahyusof
  1

• Bismark genome preparation issue

  #685 opened 2 months ago by lahyusof
  3

• Terms used in reports

  #702 opened 2 months ago by gevro
  1

• Getting strand information from/for bedGraph/coverage files

  #700 opened 3 months ago by jonasbucherETH
  1

• [help] Can Bismark handle diploid reference genome please?

  #697 opened 3 months ago by lizhe-gis
  2

• CpG count query

  #669 opened 3 months ago by MarkOEze
  6

• Failed to create directory/file when path has space: Exit 141

  #698 opened 3 months ago by llrs
  4

• [Question] Questions about adding new aligners

  #696 opened 3 months ago by YuanfengZhang
  2

• the error when dedup the sam when use the bismak

  #695 opened 3 months ago by Jiangjiangzhang6
  1

• directional and nondirectional

  #694 opened 4 months ago by iranianuser
  6

• Bismark2summary not working for output with hisat2

  #693 opened 4 months ago by JingranZhuo
  6

• index of genome faulty or non-existant

  #692 opened 4 months ago by iranianuser
  5

• deduplicate_bismark problem

  #691 opened 4 months ago by iranianuser
  4

• ambiguous results in .bam file

  #690 opened 4 months ago by iranianuser
  3

• Bismark Alignment very slow

  #670 opened 4 months ago by Nitin123-4
  11

• bismark for human genome

  #689 opened 4 months ago by iranianuser
  3

• Issue with Perl in filter_non_conversion

  #688 opened 5 months ago by edogiuili
  4

• Dose it necessary to place reads in working directory?

  #687 opened 5 months ago by iranianuser
  1

• Use SRR files with .rar (ziped) format

  #686 opened 5 months ago by iranianuser
  1

• help combining bismark pipeline with methylated UMIs

  #680 opened 6 months ago by shawpa
  8

• Spiky position in the M-Bias plot

  #673 opened 6 months ago by neolithlee
  5

• Differences in bismark convertion result

  #684 opened 5 months ago by RubioB
  1

• bismark runs to an error when I try to run it using nextflow

  #683 opened 5 months ago by Ephantus-Wambui
  4

• Parent process: Failed to build index

  #682 opened 5 months ago by yangjw1996
  3

• Expected unique alignment %

  #681 opened 5 months ago by gevro
  2

• Low unique alignment %

  #676 opened 6 months ago by gevro
  8

• How to extract methylation levels according to bam file

  #678 opened 6 months ago by myoucchent
  6

• Correcting low % methylated regions

  #679 opened 6 months ago by gevro
  4

• Analyzing spike in control performance

  #677 opened 6 months ago by gevro
  2

• Confusion on how coverage is estimated

  #675 opened 6 months ago by RJDan
  4

• Very low mapping efficiency

  #674 opened 6 months ago by gevro
  4

• Issue with bismark_genome_prep

  #672 opened 6 months ago by maf222
  7

• Execution Error

  #671 opened 6 months ago by KayaHarper
  9

• FATAL ERROR in extractor

  #668 opened 7 months ago by WYChen-penguin
  5

• Some trouble with the FastQC report

  #667 opened 8 months ago by Citrusyh
  3

• Bismark methylation extractor's bedGraph output returning ~50 million CpGs for WGBS?

  #666 opened 8 months ago by JanmajaySingh
  9

• mbias plot methylation rate fluctuations

  #664 opened 9 months ago by ertiaM
  4

• Minimum conversion efficiency for filter_non_conversion

  #663 opened 9 months ago by gevro
  1

• Bismark Extract failed always ran out of memory after 8hrs.

  #662 opened 9 months ago by RachaelAjayi
  4