When Salmon (v-0.8.2) is run on each strand of an annotation region separately (given IU as my library type), why wouldn't the TPMs be the same for each strand? From my knowledge of how read-pairs are counted, and that the library type is unstranded (yes I checked the GEO info) shouldn't the TPMS be the same... Image from sailfish docs
salmon quant -i transcripts_index --seqBias --gcBias --libType IU -1 SRR79_wt_forward.fastq -2 SRR79_wt_reverse.fastq -o SRR79_Minus_TPM
This is my first time doing RNA-Seq, any help is appreciated.