I am very new to RNA-Seq. I am trying to align my samples with STAR. I am generating the genome index myself. Because I was hoping to add the spike-in sequence to the GTF and FASTA files.
I am downloading the GTF file from here: ftp://ftp.ensembl.org/pub/release-86/gtf/mus_musculus/
There are 2 GTF files one with CHR in the name and one without. I was wondering which one should I use and how they are different. I have not figured this out just by opening the files.
If you are not sure too, would you please let me know which one you use for your analysis.
The one with CHR seems to have more lines and it seems to be scaffold genes. Am I missing something?