Hello, I have a RNAseq data(human) of 9 samples with 3 replicates each. the mapping to the reference was performed by STAR and quantification was done by RSEM. The differential expression study on genes was performed by DESeq2(taking the raw counts), but it failed for isoforms.
1) Is there some other tool with which we can perform a DE study on isoforms? 2) can we use the TPM counts instead of the raw counts for performing the DE analysis? if no. then why? 3) using tximport + deseq2 on TPM values, will this work for DE isoform study?