Question: StringTie missing header
gravatar for SarRo
17 months 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 • 630 views
ADD COMMENTlink modified 17 months ago by lakhujanivijay5.1k • written 17 months 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 17 months 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 17 months ago by genomax87k
gravatar for swbarnes2
17 months ago by
United States
swbarnes28.2k wrote:

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

ADD COMMENTlink written 17 months ago by swbarnes28.2k
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