Can you please provide your thoughts on how can I use RSEM to quantify and normalize the expression data for a set of genes and not for all the genes?
I aligned the data with STAR and got the Transcriptome BAM from it, then provide that as input to RSEM to perform the quantification and normalization. The problem with this is that the quantification and normalization were done on the entire dataset while I am just looking for the genes of interest. Because of this, the denominator for the FPKM and TPM values is much higher because of the total library size.
Hello authors,
Can you please provide your thoughts on how can I use RSEM to quantify and normalize the expression data for a set of genes and not for all the genes?
I aligned the data with STAR and got the Transcriptome BAM from it, then provide that as input to RSEM to perform the quantification and normalization. The problem with this is that the quantification and normalization were done on the entire dataset while I am just looking for the genes of interest. Because of this, the denominator for the FPKM and TPM values is much higher because of the total library size.
I hope the question is clear enough.
Thank you, Tushar