Salmon Output File Formats

Quantification File

Salmon’s main output is its quantification file. This file is a plain-text, tab-separated file with a single header line (which names all of the columns). This file is named quant.sf and appears at the top-level of Salmon’s output directory. The columns appear in the following order:

Name Length EffectiveLength TPM NumReads

Each subsequent row describes a single quantification record. The columns have the following interpretation.

  • Name — This is the name of the target transcript provided in the input transcript database (FASTA file).
  • Length — This is the length of the target transcript in nucleotides.
  • EffectiveLength — This is the computed effective length of the target transcript. It takes into account all factors being modeled that will effect the probability of sampling fragments from this transcript, including the fragment length distribution and sequence-specific and gc-fragment bias (if they are being modeled).
  • TPM — This is salmon’s estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.
  • NumReads — This is salmon’s estimate of the number of reads mapping to each transcript that was quantified. It is an “estimate” insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.

Command Information File

In the top-level quantification directory, there will be a file called cmd_info.json. This is a JSON format file that records the main command line parameters with which Salmon was invoked for the run that produced the output in this directory.

Auxiliary File

The top-level quantification directory will contain an auxiliary directory called aux (unless the auxiliary directory name was overridden via the command line). This directory will have a number of files (and subfolders) depending on how salmon was invoked.


This file contains an approximation of the observed fragment length distribution. It is a gzipped, binary file containing integer counts. The number of (signed, 32-bit) integers (with machine-native endianness) is equal to the number of bins in the fragment length distribution (1,001 by default — for fragments ranging in length from 0 to 1,000 nucleotides).