Issues

• Read headers are incomplete when all fragments within a chunk are shorter than fraglen

  alyssafrazee/polyester#86 · Filter by author MarcelloMalpighi opened on May 11, 2026
  1

• Question about run time length

  alyssafrazee/polyester#83 · Filter by author cmill221 opened on Apr 16, 2023

• Exact number for reads_per_transcript simulated reads

  alyssafrazee/polyester#81 · Filter by author Glenn032787 opened on Aug 15, 2022

• simulate_experiment discrepancy in basemean values for simulated data

  alyssafrazee/polyester#80 · Filter by author vavouri-lab opened on Jun 8, 2022

• Specifying Number of Reads Overall

  alyssafrazee/polyester#79 · Filter by author nmshahir opened on Dec 8, 2021

• Simulation of error-free reads

  alyssafrazee/polyester#77 · Filter by author hl-xue opened on Oct 6, 2021

• Support for GFF3

  alyssafrazee/polyester#76 · Filter by author TBooker opened on Aug 27, 2021
  1

• Typo in the documentation re fold_changes in simulate_experiment

  alyssafrazee/polyester#72 · Filter by author ning-y opened on Aug 23, 2020

• error in function simulate_experiment_countmat

  alyssafrazee/polyester#71 · Filter by author mhjiang97 opened on Aug 12, 2020

• simulate_experiment() fails when idfield (default: "transcript_id") is not present in the first line of the gtf file

  alyssafrazee/polyester#68 · Filter by author alorchhota opened on Oct 9, 2019

• GCbias discrepancy

  alyssafrazee/polyester#67 · Filter by author Glfrey opened on Aug 9, 2019

• A few suggestions

  alyssafrazee/polyester#66 · Filter by author sagnikbanerjee15 opened on Apr 3, 2019

• Only outputting one file?

  alyssafrazee/polyester#64 · Filter by author theheking opened on Mar 24, 2019
  5

• Read length longer than 100 with illumina4 platform error

  alyssafrazee/polyester#63 · Filter by author tonyyzy opened on Mar 22, 2019

• basemeans in simulate_experiment when num_rep == 1

  alyssafrazee/polyester#62 · Filter by author orangebromeliad opened on Mar 22, 2019
  2

• customizing positional and GC biases

  alyssafrazee/polyester#60 · Filter by author Congm12 opened on Oct 1, 2018
  3

• gcbias argument in simulate experiment

  alyssafrazee/polyester#55 · Filter by author Aslic opened on Apr 13, 2018
  1

• Output of FASTQ or QUAL in addtion to FASTA

  alyssafrazee/polyester#54 · Filter by author medcelerate opened on Mar 29, 2018
  1

• [feature request] Explicitly label mutated bases in simulated reads.

  alyssafrazee/polyester#52 · Filter by author SaraEl-Metwally opened on Jan 25, 2018
  1

• Duplicated read IDs using simulate_experiment_countmat()

  alyssafrazee/polyester#50 · Filter by author vllorens opened on Jan 16, 2018
  1

• strand specific argument

  alyssafrazee/polyester#40 · Filter by author dn070017 opened on Sep 22, 2016
  4

• Trouble changing size parameter

  alyssafrazee/polyester#37 · Filter by author rramaker opened on Sep 4, 2016
  5

• Time and memore requirements

  alyssafrazee/polyester#36 · Filter by author mw55309 opened on Aug 19, 2016
  3

• Parallelize simulate_experiment()?

  alyssafrazee/polyester#32 · Filter by author kcha opened on Feb 17, 2016

• simulate_experiment cannot handle 0 counts in transcripts

  alyssafrazee/polyester#28 · Filter by author roryk opened on Nov 4, 2015
  2