Entering edit mode
5.8 years ago
brett.vanderwerff
▴
30
I am using kallisto to analyze some RNA-seq samples.
So I know that you can get a good idea of the differential expression of isoforms across conditions downstream of kallisto using tools like sleuth and IsoformSwitchAnalyzeR. What I am wondering is if there is method or library for determining the proportion of isoforms within a condition, not across conditions.
Lets say my favorite gene has 3 isoforms (A, B, and C)
Lets say I have output from kallisto from 3 replicates of samples not treated with anything. I am really interested in knowing the proportion of A, B, and C present in this baseline condition.
Is there a good way to figure out, say for example that isoform A is the most abundant isoform in my 3 untreated samples?
Thank you.
Could you not just for each gene calculate the mean isoform expression over your 3 replicates and then look for which is the largest?
I wasn't sure because the isoforms might extract different or have different lengths which would affect the numbers of reads they get vs some other isoform from the get go. I know cross gene comparisons are kind of tricky so I thought I would ask.
Sure - you would have to use length normalized expression values such as the TPM estimated by Kallisto