pachterlab/kb_python

Issues

• Runtime error with kb count

  #266 opened a month ago by kaushik-roy-physics
  5

• using kb-python with the Takara SMART-Seq mRNA LP (with UMIs) kit

  #267 opened a month ago by franziskadenk
  2

• Error during summing matrices step

  #268 opened a month ago by palatinate
  1

• Why are UMI counts in adata.h5ad and cells_x_genes.total.mtx different?

  #265 opened 2 months ago by NaotoKubota
  4

• Obtain nascent/mature counts for 10x 5' RNA-seq

  #264 opened 2 months ago by ddiez
  0

• kb: error: unrecognized arguments: --umi-gene in version 0.28.2

  #263 opened 2 months ago by wlkath
  3

• When trying to use technology STORMSEQ - error

  #261 opened 2 months ago by yeroslaviz
  4

• I am having an issue with kb index, it won't take my files (I think ?)

  #260 opened 2 months ago by ashaypatel
  26

• Fatal error LNK 1181 when trying to install kb-python on Windows 10 system

  #256 opened 3 months ago by caj005
  1

• Barcode length of zero for custom technology strings

  #258 opened 3 months ago by mckellardw
  2

• kb-python for MARS-seq

  #252 opened 3 months ago by sam-shariati
  2

• Running kb_python for Smart-seq3 data where index files have not been provided.

  #257 opened 4 months ago by axelalmet
  4

• No reads pseudoaligned in 10XV1 chemistry

  #247 opened 4 months ago by XiaoMa55555
  6

• kb count long run time (run seems stuck)

  #255 opened 4 months ago by dsb66
  2

• Issue obtaining unaligned reads

  #250 opened 4 months ago by DanLesman
  3

• Whitelist for SMARTSEQ2 technology

  #254 opened 4 months ago by dawe
  6

• Syntax for 3-reads, paired end technology?

  #253 opened 4 months ago by dawe
  3

• Kb count command stuck on bustools count step

  #251 opened 5 months ago by gauravgadhvi
  5

• Naive collapsing of UMIs in SS3xpress data?

  #246 opened 5 months ago by biobenkj
  6

• Changed barcodes from the kb-python count

  #249 opened 5 months ago by Alvis-Jiang
  2

• Usage of f1 and f2 parameters in kb ref and count

  #248 opened 5 months ago by NikTuzov
  2

• kb ref can't handle blanks in path arguments

  #245 opened 5 months ago by NikTuzov
  2

• Crosspost from kallistobustools: kb count error with CSP reads

  #242 opened 6 months ago by kaijli
  21

• kb count - joint vs individual sample processing for RNA velocity analysis

  #244 opened 6 months ago by NikTuzov
  2

• Running kb count with a single FASTQ file

  #243 opened 6 months ago by NikTuzov
  4

• kb-python processing significantly less reads

  #241 opened 6 months ago by Celine-Serry
  6

• How to run RNA velocity analysis (La Manno) on BAM files

  #240 opened 7 months ago by NikTuzov
  4

• Containerized kb can choose the wrong binary

  #239 opened 7 months ago by gennadyFauna
  1

• --umi-gene no longer supported in kb count?

  #238 opened 7 months ago by biobenkj
  2

• SmartSeq3 Demultiplexed Fastq files

  #235 opened 7 months ago by AlisonKennedy
  4

• kb-python version 0.28.2 giving problems on m1 mac

  #236 opened 7 months ago by shashkat
  6

• Is kb-python capable of processing many samples in one command?

  #237 opened 8 months ago by shashkat
  2

• Restructure unmapped SMART-seq3 BAM from ENA to proper fastqs for kb

  #230 opened 9 months ago by biobenkj
  5

• Custom fasta and gtf file based on subset of genes for multiple species

  #231 opened 9 months ago by gracedai23
  3

• Issues with running RNA velocity (La Manno) analysis in kb_python 0.28.0

  #228 opened 9 months ago by NikTuzov
  5

• Custom Index with a new sequence

  #226 opened 9 months ago by lukais-iohan
  2

• Signals.SIGILL: 4 when running kb ref

  #222 opened 9 months ago by yquint21
  5

• kb count settings/config for the new 10x Visium (11mm capture area) dataset

  #223 opened 9 months ago by gauravgadhvi
  4

• Using kb -count with SMART-Seq mRNA LP (with UMIs)

  #229 opened 9 months ago by franziskadenk
  12

• Error when Running nac with tcc option

  #227 opened 10 months ago by bio-info-guy
  4

• Confusion regarding Intronic Sequence Generation in new 'nac' Workflow

  #225 opened 10 months ago by bio-info-guy
  4

• kallisto index file not found index.idx_cdna

  #219 opened 10 months ago by feasiblee
  3

• Effective length normalization for full-length UMI scRNA-seq data

  #218 opened a year ago by biobenkj
  8

• Support for Demultiplexed Smart-seq3 data

  #217 opened a year ago by kvn95ss
  3

• Support for SMARTSEQ3 single end data.

  #216 opened a year ago by hakobyansiras
  14

• If it doesn't exist yet, is it possible to add an option that filters the genes by abundance

  #220 opened a year ago by NikTuzov
  3

• fixed RNA profiling

  #215 opened a year ago by yfarjoun
  2

• the kb automatically terminate

  #214 opened a year ago by doudou159
  2

• Tutorial question on filtering out by mitochondrial content

  #212 opened a year ago by ScienceComputing
  5

• Tutorial question on expected_num_cells

  #211 opened a year ago by ScienceComputing
  2