I am a newbie to RNA seq and differential gene expression and I'm struggling with stringtie.
After merging all my stringtie outputs into a reference .gtf I've got same error messages for every sample.
samopen] no @SQ lines in the header. [sam_read1] missing header? Abort!
I've used the following command:
stringtie -e -B -p 4 -G /merged_gtf_location/stringie_merged.gtf -o stringtie_out.gtf sample1.gtf --rf
When I converted my hisat2 outputs into .bam files I checked for headers and also running stringtie the first time didn't give me that error. I guess it's just a very stupid mistake but I really can't figure it out on my own and I'd be really happy for any help.