Hello,

I did some googling about mRNAseq pipeline and built that pipeline. So I would like to know if my pipeline is okay.

Reference genome : Human gencode GRCh37   
Aligner : STAR  
Expression quantification : RSEM  
Gene count table convert? : tximport  
Statistical test : DESeq2  

it seems like people use htseq or featureCount for gene count table and put it into edgeR or DESeq2. I am not sure, if I go for RSEM to run DESeq2 instead of htseq or featureCount. I tried kallisto and slueth, but I want to stick to this traditional alignment method.

Any advice would be apprieciated.  
Thank you,
> I would like to know if my pipeline is okay.

RSEM can use STAR within its own script, so I would do that instead of running STAR yourself, unless you want to sophisticate your mapping more. 

> I am not sure, if I go for RSEM to run DESeq2 instead of htseq or featureCount.

The output is comparable, it's a matter of choice, perhaps RSEM is more sophisticated. But in the end it's counting mapped reads per gene/transcript. 

> I tried kallisto and slueth

Read this: http://www.rna-seqblog.com/limitation-of-alignment-free-tools-in-total-rna-seq-quantification/