Issues

• Should rsem-prepare-reference use input FASTA(s) for STAR index generation and not RSEM's .idx.fa?

  deweylab/RSEM#240 · Filter by author maxklapholz opened on Sep 6, 2026

• 1

  deweylab/RSEM#239 · Filter by author 1704925405-beep opened on Aug 12, 2026

• Issue with RSEM Index Construction for Cocos nucifera

  deweylab/RSEM#232 · Filter by author biocai123 opened on Nov 20, 2025

• rsem-tbam2gbam cannot handle SEQ="*" even when none present in unsorted .bam file

  deweylab/RSEM#231 · Filter by author MatthewRalston opened on Oct 31, 2025
  2

• Version number in rsem_perl_utils.pm not updated in v1.3.3 release?

  deweylab/RSEM#227 · Filter by author rquincyr opened on Jun 25, 2025

• Issue with Generating Paired-End Model from Real FASTQ Files

  deweylab/RSEM#226 · Filter by author QianhuiWan opened on Mar 26, 2025

• get zero count in result files

  deweylab/RSEM#225 · Filter by author wangduo-ux opened on Mar 26, 2025

• RSEM bam

  deweylab/RSEM#224 · Filter by author MarcelloMalpighi opened on Dec 25, 2024

• rsem-extract-reference-transcripts fails with "Error Message: Strand is neither '+' nor '-'!"

  deweylab/RSEM#220 · Filter by author J-Moravec opened on Aug 21, 2024

• Single-end fragment length mean and SD

  deweylab/RSEM#219 · Filter by author byqmed opened on Jul 30, 2024

• Not sure if rsem is using --num-threads option...

  deweylab/RSEM#217 · Filter by author siyer-broad opened on Jun 25, 2024

• bam only containing aligned reads produced different expression profile

  deweylab/RSEM#216 · Filter by author TwoFlowers1 opened on May 24, 2024

• rsem-generate-ngvector command not found

  deweylab/RSEM#215 · Filter by author yma122 opened on May 3, 2024
  1

• Gtf file

  deweylab/RSEM#212 · Filter by author luisafmc opened on Apr 1, 2024

• rsem-parse-alignments and rsem-build-read-index

  deweylab/RSEM#211 · Filter by author project-FSL opened on Mar 22, 2024

• rsem-prepare-reference arguments

  deweylab/RSEM#209 · Filter by author baizhantianyu opened on Feb 26, 2024

• error when using convert-sam-for-rsem to a RSEM compatible BAM file.

  deweylab/RSEM#208 · Filter by author qxf1995 opened on Feb 18, 2024

• about gffcompare

  deweylab/RSEM#205 · Filter by author fafuyyk opened on Oct 7, 2023

• Problem implementing a reverse-strand specific analysis

  deweylab/RSEM#204 · Filter by author sknaack opened on Aug 12, 2023
  2

• genomeSAsparseD option for RSEM Star?

  deweylab/RSEM#202 · Filter by author Leelab-623 opened on Jul 25, 2023

• The SAM/BAM file declares less than one reference sequence!

  deweylab/RSEM#201 · Filter by author Heterosigma opened on Jun 30, 2023
  2

• how to simulate single-end reads?

  deweylab/RSEM#200 · Filter by author yhg926 opened on Jun 9, 2023

• import using tximport for the rsem count table to get integers?

  deweylab/RSEM#199 · Filter by author marwa38 opened on Jun 8, 2023

• gene id

  deweylab/RSEM#198 · Filter by author km-2021 opened on May 29, 2023

• rsem-calculate-expression

  deweylab/RSEM#197 · Filter by author km-2021 opened on May 17, 2023