Aligning RNA-seq reads to reference genome

This tutorial introduces you to HISAT2 and STAR aligners for RNA-seq reads, and it also describes the BAM file format. You can find the course material at chipster.csc.fi/manual/course....

[@yourlifeonpower]

Thank you very much for the awesome introduction!

[@stanyang4321]

Hii!
I have three SRA data with each having different samples. So how and at what step should I merge them all together

[@ChipsterTutorials]

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.