Is there any R packages or programs could help me to calculate **effective length** of every isoform or gene? We know the importance of effective length when we calculate TPM for isoforms or genes . but we can not got it from featurecount program. Salmon can get it ,but it is only for isoforms.
If you are doing a gene-level analysis, then I recommend you simply use the gene length values that come from
The concept of effective length is for transcripts rather than genes and is not so clearly relevant for an analysis of gene-level counts from
featureCounts. However, if you wanted to modify the gene lengths in a way similar to how kallisto and Salmon modify the transcript lengths, it would simply be gene-length minus the average read length.
You cannot do that. The effective length requires isoform quantification (afterwards summing to get gene expression) which featureCounts cannot do. For featureCounts you will have to settle on FPKM normalization.
Why not just quantify with Salmon in the first place?