how to interpret very short effective length in Salmon output

Question

[hans]

Hello I am interested in a specific transcript in the quant.sf output file of Salmon. This transcript has length of 153 nt and, according to salmon, an effective length of 13-15 nt, depending on the sample. The transcript have very low counts of 26 TPM and 1 read in a sample. It seems like a big difference between the actual length and the effective length. What is the cause of such a difference and how does it effect the TPM and count output? Thank you

Answer 1

[Istvan Albert]

There are different ways to compute effective lengths for a rundown on the specific approach implemented in Salmon see the blog post by the author of Salmon:

http://robpatro.com/blog/?p=235#efflen

However, it will generally be convenient to talk about the effective length of a transcript independent of any specific fragment. In that case, what we actually mean is the expected effective length of the transcript (the effective length, in expectation, over all fragments that might derive from it). This can be computed as F = L - M where M is the mean of the empirical fragment length distribution (the observed distribution of fragments in our sample) truncated to consider only fragments of maximum length L. Given these fundamental quantities of interest, we can now discuss how they relate to the quantities that are often reported by transcript quantification tools.