The contents of the quant.genes.sf file and the quant.sf file are identical.

[happypiggyzjx]

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?
salmon (bulk mode)
Describe the bug
The contents of the quant.genes.sf file and the quant.sf file are identical.

The file quant.genes.sf should have been the results of genes quantification, but now it is all transcript quantification. I.e., the file quant.genes.sf is exactly the same as quant.sf (only the transcript names corresponding to the Name column are in a different order).

To Reproduce

• Which version of salmon was used?

• 1.10.3

• How was salmon installed (compiled, downloaded executable, through bioconda)?

• bioconda

• Which reference (e.g. transcriptome) was used?
  /hot_warm_data/wangduo/reference/Homo_sapiens.GRCh38.109.gtf
  /hot_warm_data/wangduo/reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa
  /hot_warm_data/wangduo/reference/Homo_sapiens.GRCh38.cdna.all.fa

• My options ：

• generate decoys.txt:
  grep "^>" < /hot_warm_data/wangduo/reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa | cut -d " " -f 1 >
  /cold_data/zhaojiaxin/ensembl/salmon/decoys.txt
  sed -i.bak -e 's/>//g' /cold_data/zhaojiaxin/ensembl/salmon/decoys.txt
  cat /hot_warm_data/wangduo/reference/Homo_sapiens.GRCh38.cdna.all.fa
  /hot_warm_data/wangduo/reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa >
  /cold_data/zhaojiaxin/ensembl/salmon/salmon_gentrome.fa

• salmon index
  /home/zhaojiaxin/anaconda3/envs/salmon/bin/salmon index
  --transcripts /cold_data/zhaojiaxin/ensembl/salmon/salmon_gentrome.fa
  --kmerLen 31
  --index /cold_data/zhaojiaxin/ensembl/salmon/transcripts_index
  --decoy /cold_data/zhaojiaxin/ensembl/salmon/decoys.txt
  --keepDuplicates
  --threads 50

*/home/zhaojiaxin/anaconda3/envs/salmon/bin/salmon quant
--libType A
--index /cold_data/zhaojiaxin/ensembl/salmon/transcripts_index
--unmatedReads /cold_data/zhaojiaxin/long_read/GRM/upstream-analysis/trim_polya/GRM/ONT_GRM_R01/ONT_GRM_R01.full_length.trim_polyA.filter.fasta
--output /cold_data/zhaojiaxin/ensembl/salmon/transcripts_quant
--seqBias
--gcBias
--posBias
--geneMap /hot_warm_data/wangduo/reference/Homo_sapiens.GRCh38.109.gtf
--auxDir aux_info
--incompatPrior 0
--threads 50

Expected behavior
I want the genes quantization results to appear normally in the file quant.genes.sf.

Desktop (please complete the following information):

• OS : Ubuntu Linux
• Version
  uname -a：
  Linux 1302ubuntu 6.8.0-40-generic make build more reproducible #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

lsb_release -a：
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 22.04.4 LTS
Release: 22.04
Codename: jammy

Additional context
I've already found a similar question, but it didn't solve my problem very well, the link to this question is as follows: #569. As I understand it, one of the two questioners solved the problem by updating the salmon version, the other by tximport solved the problem. But first of all my salmon version is the latest 1.10.3, and secondly, I understand that tximport is an R package that handles salmon output files, which may not solve my problem. Looking forward to your professional reply and help!