Question: Unknown Stringtie IDs produced when using Ensembl GTF
0
gravatar for freuv
2.2 years ago by
freuv20
freuv20 wrote:

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?

rna-seq stringtie ensembl gtf • 873 views
ADD COMMENTlink modified 2.2 years ago by Emily_Ensembl21k • written 2.2 years ago by freuv20

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.

ADD REPLYlink written 2.2 years ago by Emily_Ensembl21k

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

ADD REPLYlink written 2.2 years ago by freuv20

Please provide the command line.

ADD REPLYlink written 2.2 years ago by ATpoint36k
stringtie aligned.bam -v -o output.gtf -p 12 -G Mus_musculus.GRCm38.92.gtf -A abundance.txt -C fully_covered_refs.txt
ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by freuv20

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

ADD REPLYlink modified 2.2 years ago by genomax87k • written 2.2 years ago by lakhujanivijay5.1k

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

ADD REPLYlink written 2.2 years ago by freuv20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 685 users visited in the last hour