Unknown Stringtie IDs produced when using Ensembl GTF

Question

[freuv]

I quantified gene expression using an Ensembl GTF as a reference. However, the abundance estimates contain several thousand Stringtie IDs in addition to the Ensembl IDs.

Where did Stringtie pull these IDs from? How can they be converted to a more common identifier?

[Emily]

I have added the tags "Stringtie", "Ensembl" and "GTF" to your post. People on BioStars use the tags to search for questions that they might be able to answer, and follow relevant tags with My Tags, so judicious use of tags can help people to find and answer your questions. We recommend tagging with the name of the tool(s) you are trying to use, the type of analysis you're trying to do and the file-types you're working with.

[freuv]

Thank you! I will be sure to do this going forward.

[ATpoint]

Please provide the command line.

[freuv]

stringtie aligned.bam -v -o output.gtf -p 12 -G Mus_musculus.GRCm38.92.gtf -A abundance.txt -C fully_covered_refs.txt

[lakhujanivijay]

If you are talking about the MSTRG IDS, you may refer to these links

• link1
• How to deal with MSTRG tag without relevant gene name?

[freuv]

They are not MSTRG tags -- they are formatted as STRG.nnnn