What is an .sf file. What information does it contain?

  • $\begingroup$ Can you provide a little more context as to where you have seen this file and what part of bioinformatics you are working in. $\endgroup$
    – Bioathlete
    Commented Oct 29, 2019 at 20:49

1 Answer 1


You should provide more context, otherwise one can only guess what is it you are looking for! In case you are asking about Salmon's output, below is from their documentation:

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
  • $\begingroup$ Thanks. This definition helps. The file contains genomic sequence information, but I've never come across this type of file until now, and I'm not sure what tools can interpret and manipulate this type of file. $\endgroup$
    – Lou_A
    Commented Oct 29, 2019 at 19:07
  • $\begingroup$ Please edit your question and add your specific aims/questions. There are a lot of experts here that can suggest tools/workflows for your specific needs. $\endgroup$
    – haci
    Commented Oct 29, 2019 at 19:13
  • $\begingroup$ Thanks. This is helpful. I've never seen this extension before. What is Salmon generally usually used for in genomics? $\endgroup$
    – Lou_A
    Commented Oct 29, 2019 at 19:38

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.