Question: StringTie missing header
gravatar for SarRo
4 weeks ago by
SarRo0 wrote:


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.

rna-seq assembly • 125 views
ADD COMMENTlink modified 4 weeks ago by Vijay Lakhujani4.0k • written 4 weeks ago by SarRo0

Apparently I didn't. Wow, that's embarrassing! I've checked my command so many times and it really didn't occur to me... Thank you!

ADD REPLYlink written 4 weeks ago by SarRo0

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

ADD REPLYlink written 4 weeks ago by genomax65k
gravatar for swbarnes2
4 weeks ago by
United States
swbarnes25.2k wrote:

Umm, where in that command line are you telling StringTie where your bam is?

ADD COMMENTlink written 4 weeks ago by swbarnes25.2k
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