Aligning reads to reference and counting aligned reads per genes (e.g. with HTSeq) is done separate for each sample. You can then combine the count files together to a count table where the rows are genes and columns are samples. Using this table you can then look for statistically significantly differentially expressed genes with tools like DESeq2.
Thank you very much for the awesome introduction!
Hii!
I have three SRA data with each having different samples. So how and at what step should I merge them all together
Aligning reads to reference and counting aligned reads per genes (e.g. with HTSeq) is done separate for each sample. You can then combine the count files together to a count table where the rows are genes and columns are samples. Using this table you can then look for statistically significantly differentially expressed genes with tools like DESeq2.
Hi, what if there’s no reference genome then how are we supposed to do? and what are criteria to choose reference genome?