jsh58/Genrich

Issues

• Specifying Custom hg19 Genome

  #112 opened 5 months ago by phoebe460
  2

• interpretation of q value

  #111 opened 7 months ago by pengxin2019
  4

• All qvalue are -1 in narrowPeak

  #110 opened 7 months ago by pengxin2019
  7

• Peak calling missing closely located peaks?

  #80 opened 7 months ago by Simso86
  4

• Genrich on bed derived bam file

  #85 opened 7 months ago by emoiso
  3

• Genrich with large number of samples

  #91 opened 7 months ago by bwenz91
  4

• Request optional fragment length filter

  #93 opened 7 months ago by jmw86069
  2

• Can I use Genrich to call peaks from m6A (MeRIP)-seq data?

  #99 opened 7 months ago by zhiyi1988
  2

• HowTo call peaks from bigwig files?

  #103 opened 7 months ago by malcook
  2

• [Question]: Genrich ATAC-seq read-shifting peak calling

  #105 opened 7 months ago by tamuanand
  1

• IGV and Genrich issues

  #106 opened 7 months ago by ChakrabortyJC
  1

• Poorly formatted SAM record error

  #108 opened 10 months ago by rotoke
  2

• meanlog and sdlog formulas explanation

  #109 opened 7 months ago by BHB26
  1

• CUT&TAG with Genrich

  #107 opened 10 months ago by sunta3iouxos
  2

• Genrich output a broad peak file.

  #104 opened a year ago by justadustbuster
  0

• Error code: "SAM/BAM file not sorted by queryname (samtools sort -n)"

  #68 opened 4 years ago by ydchung15
  2

• Removing PCR duplications gets more peaks ?

  #101 opened a year ago by akhst7
  2

• link for awk command does not work

  #100 opened a year ago by ntsopoul
  1

• question: updating Genrich on bioconda - recent Genrich update (debug error SAM w/o sort-order)

  #102 opened a year ago by tamuanand
  0

• program failed

  #98 opened 2 years ago by lmanchon
  1

• Error! 635104 Cannot Convert to int

  #97 opened 2 years ago by tzvi909
  2

• Number of peaks fall after including input DNA control

  #94 opened 2 years ago by keenhl
  1

• Genrich with Cut & Tag samples?

  #92 opened 2 years ago by r-mashoodh
  4

• Peak Calling with a Control or without

  #74 opened 2 years ago by lilian18100
  1

• Calculation of the p-value for a comprehensive calibration of minimum AUC

  #75 opened 2 years ago by lilian18100
  1

• Peak summit

  #87 opened 2 years ago by wangxiangxiu
  1

• Handle a subset of the reference genome during peak calling

  #90 opened 2 years ago by Simso86
  1

• Description of the -v option

  #96 opened 2 years ago by Le1223
  1

• Consider fragments file as input.

  #95 opened 2 years ago by maxim-h
  2

• on determining σ for p-value calculation

  #88 opened 2 years ago by malcook
  4

• BedGraph-ish with replicates to BigWig

  #89 opened 3 years ago by Simso86
  2

• Error! Cannot parse BAM file

  #86 opened 3 years ago by birkiy
  1

• About ATAC-seq peakcalling

  #84 opened 3 years ago by ChunjieJiang
  2

• ATAC-seq pipeline

  #82 opened 3 years ago by LunaPatton
  2

• Background pileup value and AUC cutoff

  #83 opened 3 years ago by TeiturAK
  1

• "poorly formatted BED record" error on bed6 format

  #81 opened 3 years ago by lengie
  2

• Allow Genrich to use reads marked as duplicate

  #66 opened 4 years ago by dariober
  3

• understanding origin of extremely broad peaks

  #79 opened 3 years ago by malcook
  9

• peak calling with repeats

  #78 opened 3 years ago by 809825706
  3

• Discordant alignments and -y option in PE ATAC-Seq experiment

  #77 opened 3 years ago by uli-arb
  1

• Calibration of the 'Minimum AUC for a peak' for Atac-seq

  #73 opened 3 years ago by lilian18100
  4

• bwa multimap reads

  #69 opened 3 years ago by sunta3iouxos
  1

• Error! Failure in ungetc() call

  #76 opened 3 years ago by shengxin321
  2

• genrich fails with floating point error (136) on too much input

  #72 opened 3 years ago by malcook
  7

• bedgraphs normalization

  #71 opened 4 years ago by sunta3iouxos
  4

• Can not make

  #70 opened 4 years ago by GildasLepennetier
  2

• Narrow and Broad Peaks

  #65 opened 4 years ago by Carmelo-Bravo
  2

• Minimum AUC settings for different number of reads

  #63 opened 4 years ago
  1

• Is this miss expected?

  #62 opened 4 years ago by dariober
  3

• More peaks in merged replicates than the sum of single replicates

  #64 opened 4 years ago by amitjavilaventura
  1