RNA STAR analysis: Reads per gene

[cannico]

Hello everyone,

I’m currently trying to perform RNA-Seq alignment with the help of RNA STAR. I performed the alignment and I would like to export t he Reads per gene file. My question is: If I click on the reads per gene file I get 3 columns without any IDS at the top (see attached 1st picture). Hence, what exactly do these columns represent? Furthermore, should I perform additionally feature counts and then export the file (2nd picture)? I have attached the outputs for both methods attached. Thank you very much for your help!

[zee_azizah]

Hello, STAR output reads per gene gives 4 columns, they are:

1. Gene ID
2. Counts for unstranded RNA-seq
3. Counts for the 1st read strand aligned with RNA
4. Counts for the 2nd read strand aligned with RNA

I found the details here,
Reference-based RNA-Seq data analysis

go to part Counting the number …, on the Hands-on: Choose Your Own Tutorial, choose STAR