epi2me-labs/modbam2bed

Issues

• Methylation bed file output cols - Coming as 18 , description available only for 16 in readme

  #71 opened 8 months ago by snehaleela
  1

• modbam2bed N_filt

  #70 opened 8 months ago by Houssem-der
  3

• 6mA Mod calling in bacterial Data

  #69 opened a year ago by AzlanNI
  1

• Adding --aggregate flag does not result in aggregate behavior

  #68 opened a year ago by ddubocan
  1

• ERROR: --highthreshold must be larger than --lowthreshold

  #67 opened a year ago by Baix7
  1

• Dependencies

  #66 opened a year ago by NickNCL
  1

• Unexpected behavior calling `list()` on `ModBam().reads()` generator

  #50 opened a year ago by thekugelmeister
  5

• Warning message inquiry

  #65 opened a year ago by nsgarcia27
  1

• Supplying -m argument multiple times only seems to output the data from last option provided

  #25 opened a year ago by mp15
  2

• Diffrent output size for different insert bams?

  #64 opened a year ago by assafgrw
  1

• visualize in IGV

  #62 opened a year ago by sujunhao
  1

• Modified-Base calling of pod5 files with Dorado, what's next ?

  #61 opened a year ago by 120985
  1

• Correct workflow for extracting modified bases from bonito calls

  #60 opened 2 years ago by jorisbalc
  1

• modbampy

  #59 opened 2 years ago by keenhl
  2

• Modbampy Python package

  #58 opened 2 years ago by keenhl
  1

• Is there a way to mimic the "edge_filter" behavior of megalodon in modbam2bed?

  #55 opened 2 years ago by billytcl
  2

• Removal of setting canonical and mod thresholds

  #57 opened 2 years ago by pwh124
  1

• how is coverage calculated

  #56 opened 2 years ago by xiaoyunguo
  1

• ModuleNotFoundError: No module named 'libmodbampy'

  #42 opened 2 years ago by rowanhowellGE
  4

• version

  #54 opened 2 years ago by rl4940
  4

• Symbol lookup error: undefined symbol: bam_mods_at_qpos

  #52 opened 2 years ago by szakallasn3
  2

• `undefined symbol: inflate` for modbampy

  #53 opened 2 years ago by PanZiwei
  2

• ML tag can’t show the correct skipped sites number in Nanopore sequencing

  #51 opened 2 years ago by PanZiwei
  1

• No modified base tags for reads with supplementary alignments?

  #47 opened 2 years ago by PanZiwei
  12

• Don't have reference fasta

  #48 opened 2 years ago by keenhl
  6

• error while loading shared libraries: libhts.so.3

  #49 opened 2 years ago by palakela
  2

• Working with Dorado Basecaller

  #46 opened 2 years ago by ethan-mcq
  1

• How to get mapped sites number from modbam file

  #44 opened 2 years ago by PanZiwei
  1

• `modbampy.ModBam.pileup` idiosyncrasies or inconsistencies

  #45 opened 2 years ago by thekugelmeister
  4

• "make modbam2bed" fails

  #36 opened 2 years ago by ekushele
  3

• Dead link

  #40 opened 2 years ago by Shians
  1

• Question about HG002 data

  #43 opened 2 years ago by PanZiwei
  1

• Output Issues

  #41 opened 2 years ago by jchan3188
  2

• Using CRAM files is very slow (10x slower) if REF_CACHE is not configured beforehand

  #39 opened 2 years ago by Coppini
  5

• `modbam2bed` with or without `--aggregate`?

  #35 opened 2 years ago by PanZiwei
  1

• Install modbam2bed via anaconda

  #38 opened 2 years ago by ekushele
  3

• about CpG number in modbam2bed output

  #37 opened 2 years ago by kaanokay
  2

• [E::fai_retrieve] Failed to retrieve block: unexpected end of file

  #34 opened 2 years ago by PanZiwei
  6

• pip install fails on MacOS

  #33 opened 2 years ago by marcpaga
  3

• How to interpret 0-255 methylation score

  #32 opened 2 years ago by marcpaga
  2

• Hi cjw85,

  #21 opened 2 years ago by cjw85
  1

• how to deal with many bam files

  #31 opened 2 years ago by Aline-Git
  2

• How to modified the value in pos_mod

  #30 opened 2 years ago by JeremyQuo
  3

• How to covert a bedMthy to modbam?

  #29 opened 2 years ago by JeremyQuo
  1

• CIGAR and query sequence lengths differ for

  #28 opened 2 years ago by charliechen912ilovbash
  3

• what is the difference between acc.bed and .bed file?

  #27 opened 2 years ago by AlineMuyle
  2

• No output

  #26 opened 2 years ago by charliechen912ilovbash
  2

• unaligned bam

  #24 opened 2 years ago by rrazaghi
  5

• error when installing via conda

  #23 opened 2 years ago by Jane-Gibson
  2

• More choices for modified base calls (feature request)

  #20 opened 3 years ago by sathish-t
  7