Hi all,
I was reading a paper (doi: 10.1016/j.molcel.2019.04.034). They did something interesting which caught my attention but I'm not able to comprehent properly. can someone help me to understand the following information.
To calculate change in weighted transcript length, we quantified transcript expression using Salmon v0.8.2. We then used the TxImport package (https://bioconductor.org/packages/3.4/bioc/html/tximport.html) to calculate the expression weighted transcript length for each gene. Change in length for each gene was calculated as the log2 ratio of mean length in condition transfected cells divided by mean length in control transfected cells.
If I understood correctly, they used salmon to quantify the transcript expression . Then tximport was used to generate the gene-level.
txi <- tximport(files, type="salmon", tx2gene=tx2gene[,c("tx_id", "ensgene")], countsFromAbundance="lengthScaledTPM")
but I do not understand ength for each gene was calculated as the log2 ratio of mean length in condition transfected cells divided by mean length in control. Because txi object already has the gene length. So it can be compared directly or the salmon output gives effective length of each transcript.
Am I missing something.
