This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Significance of giving read group when using hisat2

I am doing RNA-seq data analysis using hisat2 and stringTie. The purpose of my study is to search for genes that are differentially expressed between groups.

I have heard that hisat2 can add a read group by using the -rg option. I have not used the -rg option so far and have not experienced any problems. So I would like to ask, what is the significance of implementing -rg in hisat2? Would there be any inconvenience in performing a differential gene expression analysis without it? I would appreciate it if you could enlighten me.

rna-seq

1 answer

You do not need read groups for this at all. RGs are required by some tools, especially in the context of variant calling.

Thank you for your advice! I'm relived.

Log in to answer this question.