Hoohm/CITE-seq-Count

Issues

• Gene and Antibody both have a pair of fastq files, how to run CITE-seq-Count?

  #189 opened 10 months ago by edceeyuchen
  2

• Filtering UMIs on read number

  #151 opened 4 months ago by rule-110
  1

• CITE-seq R1 length issue

  #194 opened 4 months ago by Rimanpreet1
  11

• CITE-seq-Count run gets stuck

  #191 opened 9 months ago by Layla-R
  4

• different results each the CITE-seq count is run

  #165 opened 3 years ago by colin986
  5

• ValueError: columns cannot be a set

  #192 opened 8 months ago by 77babyy
  3

• Please, trim all sequences at the same length.

  #190 opened 10 months ago by edceeyuchen
  0

• Does not compile using Python version > 3.9.x please fix.

  #188 opened a year ago by TheRealQuantumCheese
  0

• Unable to locate temp file while merging results

  #187 opened a year ago by xmi215
  0

• Running Cite-Seq-count with next GEM protocol

  #181 opened a year ago by yeroslaviz
  2

• Allow to split fastq or get list of readID per cell

  #184 opened a year ago by lldelisle
  2

• Pandas error after correcting UMIs

  #183 opened a year ago by ejohnson643
  1

• Include path to tag file in run report

  #179 opened a year ago by johnyaku
  1

• ValueError: columns cannot be a set

  #172 opened 2 years ago by jamesboot
  5

• Cell Hashing on Multiome samples

  #174 opened 2 years ago by bassanio
  11

• bug in preprocessing.py -> get_read_paths() (version 1.4.3)

  #175 opened a year ago by AlexSurnov
  1

• method keeps looking for whitelist when not provided.

  #176 opened a year ago by naila53
  8

• barcodes with 0s in all protein tags and unmapped roll

  #180 opened 2 years ago by Hanxi-002
  2

• Discussion question -- is it normal to take so long?

  #178 opened 2 years ago by dagarfield
  3

• CITE-seq-Count for multimodal data

  #166 opened 3 years ago by YingzhengXu
  8

• 100% unmapped

  #177 opened 2 years ago by yls2g13
  0

• Python error when there are too many cells? Script never finishes

  #173 opened 2 years ago by ejagoda14
  2

• Code for running multiple lanes

  #171 opened 2 years ago by leeanapeters
  0

• Percentage unmapped: 100

  #167 opened 3 years ago by sopenaml
  18

• Different "UMIs corrected" results between v1.4.3 and v1.4.5

  #169 opened 3 years ago by rosaxma
  2

• Complex whitelist

  #168 opened 3 years ago by alanaleah89
  2

• error running cite-seq-count

  #150 opened 4 years ago by fouerghi
  10

• running with totalseqB

  #158 opened 4 years ago by naila53
  4

• Could you clarify internal QC in CITE-seq-Count?

  #141 opened 4 years ago by marianaql
  2

• Issue with No module named 'Levenshtein'

  #164 opened 3 years ago by Lopiniatre
  2

• Max memory limit when running CITE-seq-Count

  #163 opened 3 years ago by molybdenumt
  1

• CITE-seq-Count 100% unmapped

  #161 opened 3 years ago by carbycrab
  9

• Low overlap between cell barcodes and hashtag barcodes

  #159 opened 3 years ago by mary77
  2

• Confusion about input arguments

  #149 opened 3 years ago by YingzhengXu
  4

• unmapped tags

  #143 opened 4 years ago by leandrofmoreno
  11

• Understanding [expected cells] parameter and [whitelist] parameter

  #155 opened 4 years ago by jhjlee
  2

• Proper Saturation Rate Calculation

  #160 opened 3 years ago by brindavjk
  1

• Repeated MemoryError in each ForkPoolWorker

  #162 opened 3 years ago by amber4mint
  0

• Mapped/Unmapped Reads

  #156 opened 4 years ago by jamesboot
  2

• Error when option are set to --bc_collapsing_dist 0

  #157 opened 4 years ago by rule-110
  2

• Running CITE-seq-Count on ASAP-seq

  #154 opened 4 years ago by jhjlee
  7

• How can I handle with a separated cell barcode sequence?

  #153 opened 4 years ago by suzuki-shm
  3

• barcode bug

  #152 opened 4 years ago by craigamartens
  1

• Excessive memory use in apply_async causing pool to crash

  #148 opened 4 years ago by jhasselmann808
  5

• Script won't complete

  #145 opened 4 years ago by curtisd0886
  7

• v1.5.0 resulting in much lower umi counts than v1.4.4 with same settings..?

  #147 opened 4 years ago by Erinke89
  4

• line 592 of processing.py gives UnboundLocalError in 1.5.0

  #144 opened 4 years ago by Erinke89
  9

• Approximate the cell ranger unfiltered counts output?

  #146 opened 4 years ago by bbimber
  1

• -cells/--expected_cells still required when -wl provided?

  #142 opened 4 years ago by bbimber
  4

• installation issue

  #140 opened 4 years ago by hartlama
  0