Issues

• Summing position and read length exceeds chromosome size?

  BirolLab/NanoSim#257 · Filter by author IsabelMarleen opened on Jun 11, 2026
  3

• Cannot simulate transcriptomic reads with intron retention

  BirolLab/NanoSim#253 · Filter by author SimonHegele opened on Apr 15, 2026
  5

• Mismatch in read quality between input and simulated reads

  BirolLab/NanoSim#247 · Filter by author ezherman opened on Jul 17, 2025
  2

• ValueError: maximum supported dimension for an ndarray is 32, found 400000

  BirolLab/NanoSim#246 · Filter by author npdungca opened on Jul 13, 2025

• Error when FASTQ read headers are too long

  bugenhancement
  BirolLab/NanoSim#245 · Filter by author AntonS-bio opened on May 6, 2025
  1

• Non-zero error rates for perfect reads

  question
  BirolLab/NanoSim#244 · Filter by author SimonHegele opened on Mar 31, 2025
  2

• FileNotFoundError: No such file or directory when using pre-trained model

  BirolLab/NanoSim#243 · Filter by author florenmartino opened on Mar 6, 2025

• Metagenomic mode Help with read_analysis.py

  BirolLab/NanoSim#240 · Filter by author florenmartino opened on Nov 21, 2024
  1

• Feature Request: Checking Input-files

  enhancement
  BirolLab/NanoSim#239 · Filter by author SimonHegele opened on Nov 20, 2024
  1

• Transcript ID in reference and expression profile do not match

  bug
  BirolLab/NanoSim#237 · Filter by author SimonHegele opened on Oct 30, 2024
  8

• How many threads and memories required at training stage?

  BirolLab/NanoSim#236 · Filter by author yaoxkkkkk opened on Oct 20, 2024
  1

• head_vs_ht_ratio = head_vs_ht_ratio_list[each_read] IndexError: list index out of range

  BirolLab/NanoSim#228 · Filter by author huangxin0221 opened on Sep 29, 2024
  4

• KeyError: "tag 'MD' not present"

  BirolLab/NanoSim#225 · Filter by author mochew opened on Sep 25, 2024
  5

• How to simulate amplicon-seq data?

  BirolLab/NanoSim#221 · Filter by author capoony opened on Sep 8, 2024

• gzip intermediate fastq files

  feature request
  BirolLab/NanoSim#211 · Filter by author nicolo-tellini opened on Jul 12, 2024

• Stuck at the simulation step

  bug
  BirolLab/NanoSim#210 · Filter by author HLHsieh opened on Jul 10, 2024
  5

• Failure in using Nanosim for transcriptome (ValueError: file does not contain alignment data)

  BirolLab/NanoSim#208 · Filter by author aerusakovich opened on May 6, 2024

• Questions about the usage and processing of the expression profile

  feature request
  BirolLab/NanoSim#207 · Filter by author joyceFunk123 opened on Apr 18, 2024
  1

• IndexError: list index out of range

  bugquestion
  BirolLab/NanoSim#202 · Filter by author weishwu opened on Feb 16, 2024
  4

• Options / suggestions for how to simulate nCats data?

  feature request
  BirolLab/NanoSim#200 · Filter by author tfenne opened on Nov 29, 2023
  1

• Stuck at simulation stage

  bug
  BirolLab/NanoSim#193 · Filter by author kainth-amoldeep opened on May 31, 2023
  4

• ValueError: Found array with 0 sample(s) (shape=(0, 1)) while a minimum of 1 is required.

  BirolLab/NanoSim#190 · Filter by author Dr-bioinfo opened on May 16, 2023
  6

• Option to specify desired read coverage or sequencing depth

  feature requestquestion
  BirolLab/NanoSim#188 · Filter by author HLHsieh opened on Mar 31, 2023
  2

• Nanosim hangs in the middle

  bughelp wantedquestion
  BirolLab/NanoSim#184 · Filter by author aastha-batta opened on Feb 17, 2023
  18

• Can NanoSim be applied to simulate single cell Nanopore reads

  enhancementfeature request
  BirolLab/NanoSim#180 · Filter by author yuntianf opened on Jan 10, 2023
  1