a-slide/NanoCount

Issues

• Raw counts for downstream analysis

  #24 opened a year ago by lubitelpospat
  2

• nanocount for two condition

  #15 opened 2 years ago by rezarahman12
  7

• Can I directly map reads directly to genes instead of transcripts to estimate the expression in gene level?

  #37 opened 2 months ago by kerenzhou062
  1

• How do NanoCount deal with reads with multiple alignments?

  #36 opened 4 months ago by kerenzhou062
  3

• Nanocount vs Flair

  #28 opened a year ago by sagnikbanerjee15
  3

• ERROR: No valid secondary alignments found in bam file. Were the reads aligned with minimap `-p 0 -N 10` options ?

  #35 opened 6 months ago by lborcard
  1

• How can I obtain the raw file containing reads assigned to isoforms?

  #34 opened 6 months ago by zhenyu7500
  1

• Normalised the reads count

  #33 opened 7 months ago by M-Chi-1
  1

• Est_count doesn't match records

  #32 opened 10 months ago by KunFang93
  3

• Identical tpm values for different transcripts

  #29 opened 10 months ago by chloebonenfant
  2

• High % of reads lost due to discarded negative strand and invalid 3' end.

  #30 opened 10 months ago by NStrowbridge
  2

• transcript_name is chromosome name instead of gene name

  #31 opened a year ago by KunFang93
  1

• Transcript expression level to Gene expression

  #27 opened a year ago by vetmohit89
  0

• High % of sequences lost in discarded negative strand alignments

  #23 opened a year ago by NStrowbridge
  3

• Too many reads are discarded

  #26 opened a year ago by vetmohit89
  1

• How to deal with multiple ensemble IDs mapping to one gene symbol in a RNA-Seq dataset

  #25 opened a year ago by vetmohit89
  1

• Adding option for cDNA reads

  #12 opened 2 years ago by camillaugolini-iit
  3

• Why NanoCount needs sorted alignments?

  #20 opened 2 years ago by callumparr
  2

• -N 100 hinder NanoCount accuracy?

  #19 opened 2 years ago by callumparr
  2

• alignmnet using sequin reference

  #18 opened 2 years ago by rezarahman12
  1

• nanocount fast5 files

  #17 opened 2 years ago by rezarahman12
  1

• about data of nanocount paper

  #16 opened 2 years ago by rezarahman12
  1

• Different options when using minimap

  #14 opened 2 years ago by Tomcxf
  2

• Minimum number of ONT reads per sample

  #13 opened 2 years ago by ms-gx
  1

• Setting -3 to -1 to deactivate fails

  #11 opened 3 years ago by josiegleeson
  2

• No valid secondary alignment found in bam file

  #10 opened 3 years ago by jhwan1203
  1

• Using with custom filtered alignments

  #8 opened 4 years ago by josiegleeson
  5

• ZeroDivisionError: division by zero

  #5 opened 4 years ago by callumparr
  6

• Write a usage notebook instead of having usage in the README

  #2 opened 4 years ago by a-slide
  0

• TPM values do not sum up to 1 million

  #3 opened 4 years ago by lpryszcz
  1

• Extract all references and length

  #1 opened 4 years ago by a-slide
  0

• Question about normalisation

  #4 opened 4 years ago by tleonardi
  2